plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID: Plot force-directed graph with the expression of multiple...

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

Plot force-directed graph with the expression of multiple gene sets on selected sample IDs

Description

Plot force-directed graph with the expression of multiple gene sets on selected sample IDs

Usage

plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID(
  object,
  gmt.file = c(),
  selected.sampleID = c(),
  title = "",
  show_gene_sets = c(),
  custom_color = c(),
  IsDownsample = F,
  downsample.size = 0,
  isNormalizedByHouseKeeping = T,
  vertex.size = 1.5,
  edge.size = 0.2,
  edge.color = "gray",
  title.color = "red",
  title.font.size = 16,
  showLegend = T,
  background.color = "white"
)

Arguments

object	The SingCellaR object.
gmt.file	The GMT file.
selected.sampleID	Selected sample IDs
title	The title of the plot.
show_gene_sets	The name of gene sets to be shown.
custom_color	The vector of cutom color to specify gene sets.
IsDownsample	is logical. If TRUE, the cells will be downsampled.
downsample.size	The number of cells for the downsample. Default 0
isNormalizedByHouseKeeping	is logical. If TRUE, the gene expression will be normalized by the expression of house keeping genes.
vertex.size	The point size. Default 1.5
edge.size	The edge size. Default 0.2
edge.color	The edge color. Default gray
title.color	The color of the title. Default red
title.font.size	The title font size. Default 16
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.