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Plot integration benchmark results

Source: R/IntegrationBenchmarkPlot.R
IntegrationBenchmarkPlot.Rd

Visualize a Seurat object returned by RunIntegrationBenchmark(). "box" compares per-cell LISI scores across methods, "heatmap" shows scaled summary metrics, "scatter" plots the bio-vs-batch trade-off, and "umap" draws batch and cell-type embeddings. "auto" returns all of these plots.

Usage

IntegrationBenchmarkPlot(
  srt,
  plot_type = c("auto", "box", "heatmap", "scatter", "umap"),
  tool_name = "IntegrationBenchmark",
  metrics = NULL,
  palette = "Chinese",
  palcolor = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  pt.size = NULL,
  pt.alpha = 1,
  boxplot_jitter = FALSE,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object from RunIntegrationBenchmark(). "box" can also plot any metadata columns ending in "_LISI".

plot_type

Plot type, or "auto" for a named list of all views.

tool_name

srt@tools entry created by RunIntegrationBenchmark().

metrics

Optional metric names used in the heatmap.

palette, palcolor

Palette name (thisplot::show_palettes) or custom colors.

theme_use, theme_args

Theme name or function, plus extra theme arguments.

pt.size, pt.alpha

Point size and transparency. pt.size = NULL scales with sqrt(n) (minimum 0.3). Rasterized points keep at least a two-pixel radius at raster.dpi = c(512, 512) and scale with raster.dpi.

boxplot_jitter

Whether to overlay jittered points on the LISI boxes.

verbose

Whether to print the message. Default is TRUE.

...

The message to print.

Value

A ggplot, patchwork, or a named list of plots when plot_type = "auto".

See also

RunIntegrationBenchmark, RunLISI

Examples

srt <- SeuratObject::CreateSeuratObject(
  counts = Matrix::Matrix(
    matrix(1:20, nrow = 2, dimnames = list(c("g1", "g2"), paste0("c", 1:10))),
    sparse = TRUE
  )
)
set.seed(1)
srt$Uncorrected_tech_LISI <- stats::runif(10, 1.0, 1.4)
srt$Harmony_tech_LISI <- stats::runif(10, 2.0, 2.8)
srt$Uncorrected_celltype_LISI <- stats::runif(10, 1.0, 1.2)
srt$Harmony_celltype_LISI <- stats::runif(10, 1.0, 1.3)
srt@tools$IntegrationBenchmark <- list(
  summary = data.frame(
    method = c("Uncorrected", "Harmony"),
    bio = c(0.80, 0.82),
    batch = c(0.20, 0.70),
    overall = c(0.56, 0.77),
    status = "success",
    stringsAsFactors = FALSE
  ),
  metrics = data.frame(
    method = rep(c("Uncorrected", "Harmony"), each = 2),
    metric = rep(c("iLISI", "cLISI"), 2),
    category = rep(c("batch", "bio"), 2),
    value = c(1.2, 1.1, 2.4, 1.2),
    scaled = c(0.1, 0.9, 0.7, 0.85),
    direction = "higher",
    stringsAsFactors = FALSE
  ),
  runs = data.frame(
    method = c("Uncorrected", "Harmony"),
    status = "success",
    umap = NA_character_,
    stringsAsFactors = FALSE
  ),
  batch = "tech",
  celltype = "celltype"
)
thisplot::print_colored_table(
  srt@tools$IntegrationBenchmark$summary,
  by = "row",
  palette = "Chinese"
)
#> method       bio   batch  overall  status 
#> Uncorrected  0.80  0.2    0.56     success
#> Harmony      0.82  0.7    0.77     success
IntegrationBenchmarkPlot(srt, plot_type = "box")

IntegrationBenchmarkPlot(srt, plot_type = "heatmap")

IntegrationBenchmarkPlot(srt, plot_type = "scatter")