Plot LISI scores

Backward-compatible wrapper around BenchmarkPlot() for LISI scores. Visualize LISI scores on a dimensional reduction and compare methods with a summary boxplot.

Usage

LISIPlot(
  srt,
  features = NULL,
  tool_name = NULL,
  reduction = NULL,
  plot_boxplot = TRUE,
  boxplot_jitter = FALSE,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  pt.size = NULL,
  pt.alpha = 1,
  palette = "Chinese",
  palcolor = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  verbose = TRUE,
  ...
)

Arguments

srt: A Seurat object.
features: Metadata columns containing LISI scores. Default is NULL, which will use columns stored in tool_name, or all metadata columns ending with "_LISI" when tool_name is NULL.
tool_name: Tool entry created by RunLISI(). Default is NULL.
reduction: Dimensional reduction used for feature plots. If NULL, the reduction recorded in tool_name is used when available; otherwise DefaultReduction() is used.
plot_boxplot: Whether to add boxplots. Default is TRUE.
boxplot_jitter: Whether to overlay jittered points on boxplots. Default is FALSE.
combine: Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow: Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
ncol: Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
byrow: Whether to arrange the plots by row in the combined plot. Default is TRUE.
pt.size: The size of the points in the plot.
pt.alpha: The transparency of the data points. Default is 1.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".
palcolor: Custom colors used to create a color palette. Default is NULL.
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
verbose: Whether to print the message. Default is TRUE.
...: The message to print.

Value

If combine = TRUE, returns a combined patchwork plot. If combine = FALSE, returns a named list of ggplot objects.

Usage

Arguments

Value

See also