plotGenesRank: Plot the genes ranked by expression

In LabexCortexBioinformatics/LxCxUtils: Utils Function for Labex Cortex Bioinformatics Platform

Plot the genes ranked by expression

Description

Genes will be ranked by expression, and then plotted, with x axis being the rank and y axis the average expression in the cells, for each ident in group.by. Some genes will then be highlighted.

Usage

plotGenesRank(
  seur,
  genes_highlight = c(),
  group.by = "All cells",
  assay = "RNA",
  slot = "data",
  cols = NULL,
  nudge_x = "middle",
  ncol = 2,
  write_name = TRUE,
  point_size = 2,
  return_table = FALSE
)

Arguments

seur	Seurat object to use.
genes_highlight	List of genes to highlight. If some genes are not found in the dataset, they will just not be plotted.
group.by	Which ident to group the data by. Default to "orig.ident". Can also be "All cells" to get every cells in the same plot.
assay	Assay to use. Default to "RNA"
slot	slot to take the data from. Using data will assume that the data are log1p normalized, and thus will exp1p them before getting the average expression. Default to "data"
nudge_x	either a number or "middle". Will nudge the gene name on the right if positive and left if negative. Middle will try to align the gene names in the middle. Default to 2
ncol	number of column to plot, only useful if more than 1 ident. Default to 2
write_name	Whether to write the gene names or not
point_size	The size of the points. Default to 2
return_table	return a data frame containing the data used for the plot. Only works with group.by = "All cells"
colmap	colmap to use for each ident. Default to hue_pal()

Value

a ggplot object if only one ident, or a gridExtra object if more than one ident.

LabexCortexBioinformatics/LxCxUtils documentation built on Aug. 2, 2022, 6:23 a.m.