plot_tsne_label_by_multiple_gene_sets_with_limited_sampleID: Plot TSNE with the expression of multiple gene sets on...

View source: R/SingleCellPlots.R

plot_tsne_label_by_multiple_gene_sets_with_limited_sampleIDR Documentation

Plot TSNE with the expression of multiple gene sets on selected sample IDs

Description

Plot TSNE with the expression of multiple gene sets on selected sample IDs

Usage

plot_tsne_label_by_multiple_gene_sets_with_limited_sampleID(
  object,
  gmt.file = c(),
  selected.sampleID = c(),
  title = "",
  show_gene_sets = c(),
  custom_color = c(),
  isNormalizedByHouseKeeping = T,
  IsDownsample = F,
  downsample.size = 0,
  title.color = "red",
  title.font.size = 16,
  point.size = 2,
  showLegend = T,
  background.color = "white"
)

Arguments

object

The SingCellaR object.

gmt.file

The GMT file.

selected.sampleID

Selected sample IDs

show_gene_sets

The name of gene sets to be shown.

custom_color

The vector of cutom color to specify gene sets.

isNormalizedByHouseKeeping

is logical. If TRUE, the gene expression will be normalized by the expression of house keeping genes.

IsDownsample

is logical. If TRUE, the cells will be downsampled.

downsample.size

The number of cells for the downsample. Default 0

title.color

The color of the title. Default red

title.font.size

The title font size. Default 16

point.size

The point size. Default 2

showLegend

is logical. If TRUE, the figure legend will be displayed.

background.color

The background color. Default white


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