Run SpaNorm spatial normalization

Normalize spatial transcriptomics counts with the optional Bioconductor SpaNorm backend and store the normalized expression in a new Seurat assay.

Usage

RunSpaNorm(
  srt,
  assay = NULL,
  layer = "counts",
  image = NULL,
  coord.cols = c("col", "row"),
  new_assay = "SpaNorm",
  tool_name = "SpaNorm",
  store_results = TRUE,
  store_spe = FALSE,
  verbose = TRUE,
  coordinate_space = c("raw", "legacy_display"),
  ...
)

Arguments

srt

A Seurat object.

assay

Assay to use. NULL uses the default assay.

layer

Assay layer used for expression values.

image

Spatial image name. Required when multiple images are present; a single image is selected automatically when NULL.

coord.cols

Metadata coordinate columns used when no image is available.

new_assay

Name of the assay used to store SpaNorm-normalized data.

tool_name

Name used to store detailed SpaNorm results in srt@tools.

store_results

Whether to store the full result in srt@tools.

store_spe

Whether to store the backend SpatialExperiment returned by SpaNorm.

verbose

Whether to print the message. Default is TRUE.

coordinate_space

Coordinate system supplied to SpaNorm. The default is raw acquisition coordinates; use "legacy_display" explicitly to reproduce the display-scaled coordinates used before scop 0.9.0.

...

Additional arguments passed to SpaNorm::SpaNorm(), such as sample.p.

Value

A Seurat object with SpaNorm-normalized expression stored in new_assay. When store_results = TRUE, parameters, coordinates, features, cells, and optional backend output are stored in srt@tools[[tool_name]].

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)

SpatialSpotPlot(
  spatial,
  features = rownames(spatial)[1:2],
  assay = "Spatial",
  layer = "data",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)


spatial <- RunSpaNorm(
  spatial,
  assay = "Spatial",
  layer = "counts",
  coord.cols = c("x", "y"),
  new_assay = "SpaNorm",
  store_spe = FALSE,
  sample.p = 0.25,
  verbose = FALSE
)
#> (1/2) Fitting SpaNorm model
#> 496 cells/spots sampled to fit model
#> Downloading uv...
#> Done!
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, log-likelihood: -2938987.573646
#> iter:  1, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  1, log-likelihood: -2938987.573646
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  2, log-likelihood: -2484176.054998
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  3, log-likelihood: -2402166.178130
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  4, log-likelihood: -2375361.642407
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  5, log-likelihood: -2355940.158608
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  6, log-likelihood: -2345714.135668
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  7, log-likelihood: -2340815.707509
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  8, log-likelihood: -2338049.355727
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter:  9, log-likelihood: -2336724.051391
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 10, log-likelihood: -2335777.998794
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 11, log-likelihood: -2335405.319503
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 12, log-likelihood: -2334986.930904
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  1, iter: 13, log-likelihood: -2334895.607071 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, log-likelihood: -2322448.545701
#> iter:  2, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, iter:  1, log-likelihood: -2322448.545701
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, iter:  2, log-likelihood: -2319898.734858
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  2, iter:  3, log-likelihood: -2319842.159484 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, log-likelihood: -2319858.698816
#> iter:  3, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, iter:  1, log-likelihood: -2319858.698816
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, iter:  2, log-likelihood: -2319593.741850
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  3, iter:  3, log-likelihood: -2319587.504316 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, estimating gene-wise dispersion
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, log-likelihood: -2319571.561694
#> iter:  4, fitting NB model
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, iter:  1, log-likelihood: -2319571.561694
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, iter:  2, log-likelihood: -2319488.302959
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  4, iter:  3, log-likelihood: -2319476.271175 (converged)
#> Hint: To use tensorflow with `py_require()`, call `py_require("tensorflow")` at the start of the R session
#> iter:  5, log-likelihood: -2319476.271175 (converged)
#> (2/2) Normalising data

SpatialSpotPlot(
  spatial,
  features = rownames(spatial[["SpaNorm"]])[1:2],
  assay = "SpaNorm",
  layer = "data",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)