Skip to contents

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(
  object,
  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,
  ...,
  srt = NULL
)

Arguments

object

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.

combine

Combine plots with patchwork. combine = FALSE returns a list of ggplots.

nrow

Combine plots with patchwork. combine = FALSE returns a list of ggplots.

ncol

Number of columns of the combined plot.

verbose

Whether to print the message. Default is TRUE.

...

The message to print.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

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

See also

RunIntegrationBenchmark, RunLISI

Examples

if (FALSE) { # \dontrun{
data(panc8_sub)
panc8_sub <- RunIntegrationBenchmark(
  panc8_sub,
  batch = "tech",
  celltype = "celltype",
  methods = c("Uncorrected", "Harmony"),
  nHVF = 500,
  linear_reduction_dims = 20,
  linear_reduction_dims_use = 1:10,
  perplexity = 10
)
IntegrationBenchmarkPlot(panc8_sub)
IntegrationBenchmarkPlot(panc8_sub, plot_type = "box")
IntegrationBenchmarkPlot(panc8_sub, plot_type = "heatmap")
IntegrationBenchmarkPlot(panc8_sub, plot_type = "scatter")
} # }