plot_forceDirectedGraph_label_by_multiple_gene_sets: Plot force-directed graph with the expression of selected...

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 selected multiple gene sets

Description

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

Usage

plot_forceDirectedGraph_label_by_multiple_gene_sets(
  object,
  gmt.file = c(),
  show_gene_sets = c(),
  custom_color = c(),
  isNormalizedByHouseKeeping = T,
  vertex.size = 1.5,
  showEdge = T,
  edge.size = 0.2,
  edge.color = "gray",
  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.
showEdge	is logical. If TRUE, the graph's edges will be displayed.
edge.size	The size of the edge. Default 0.2
edge.color	The edge color. Default gray
showLegend	is logical. If TRUE, the figure legend will be displayed.
background.color	The background color. Default white
vertext.size	The node size. Default 1.5

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