plot_diffusionmap_label_by_multiple_gene_sets: Plot diffusion map with the expression of multiple gene sets

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Plot diffusion map with the expression of multiple gene sets

Description

Plot diffusion map with the expression of multiple gene sets

Usage

plot_diffusionmap_label_by_multiple_gene_sets(
  object,
  gmt.file = c(),
  show_gene_sets = c(),
  custom_color = c(),
  isNormalizedByHouseKeeping = T,
  x_eigenVal = "DC1",
  y_eigenVal = "DC2",
  point.size = 1,
  showLegend = T,
  background.color = "white"
)

Arguments

object	The SingCellaR object.
gmt.file	The GMT file for gene sets.
show_gene_sets	The names of selected gene sets.
custom_color	The custom color names.
isNormalizedByHouseKeeping	is logical. If TRUE, the gene expression will be normalized by the expression of house keeping genes.
x_eigenVal	The diffusion map dimension on x axis. Default DC1
y_eigenVal	The diffusion map dimension on y axis. Default DC2
point.size	The point size. Default 1
showLegend	is logical. If TRUE, the figure legend will be shown.
background.color	The background color of the plot. Default white

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.