plot_cmp_genesets: Plot the result of compare_genesets

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Plot the result of compare_genesets

Description

This function plots the results of compare_genesets.

Usage

plot_cmp_genesets(
  set_1 = NULL,
  set_2 = NULL,
  stat = c("jaccard", "hypergeom", "intersection", "union", "size_set_1", "size_set_2",
    "diff_set_1", "diff_set_2"),
  transform = c("None", "log10", "log2", "-log10", "-log2"),
  colors = colors_for_gradient("Ju1"),
  layout = c("raster", "square"),
  background = NULL,
  coord_equal = TRUE
)

Arguments

set_1	A list containing gene sets to be compared.
set_2	A list containing gene sets to be compared.
stat	The statistics to be computed between gene sets. It can be either "jaccard", "hypergeom", "intersection" "size_set_1", "size_set_2", "diff_set_1" (specific to set_1), "diff_set_2" (specific to set_2). The background is taken into account. Note that hypergeometric tests check for enrichment.
transform	The transformation to be applied to the values. It can be either "NA", "log10", or "log2", "-log10", "-log2.
colors	The color palette to be used in the plot.
layout	The type of diagram. Either "raster" (a scatter plot showing the statistics of interest) or "square". The "square" layout shows the hypergeometric pvalue (color) and the Jaccard result (size of the square).
background	The background (universe) to consider. Default to the non-redundant list of elements merged from set_1 and set2. You may provide a vector with all genes of the genome for instance.
coord_equal	make sure that the an equal length on both axis represents the same change in units

Details

see compare_genesets.

Value

A ggplot object representing the comparison results.

Examples

set.seed(123)
set_1 <- list(letters[1:10], letters[11:20], letters[21:30])
x <- sample(letters[1:30])
set_2 <- list(x[1:5], x[6:20], letters[21:30])
res <- compare_genesets(set_1, set_2, stat = "jaccard")
plot_cmp_genesets(set_1, set_2, stat = "jaccard")
plot_cmp_genesets(set_1, set_2, stat = "hypergeom", transform = "log10")
plot_cmp_genesets(set_1, set_2, layout="square", transform = "-log10")

dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.