plot_forceDirectedGraph_label_by_a_signature_gene_set: Plot force-directed graph with the expression of a gene set

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 a gene set

Description

Plot force-directed graph with the expression of a gene set

Usage

plot_forceDirectedGraph_label_by_a_signature_gene_set(
  object,
  gene_list = c(),
  gene_set_name = c(),
  isNormalizedByHouseKeeping = F,
  vertex.size = 0.5,
  vertex.color1 = "blue",
  vertex.color2 = "red",
  edge.size = 0.2,
  edge.color = "gray",
  vertex.base.color = "gray35",
  background.color = "white"
)

Arguments

object	The SingCellaR object.
gene_list	The vector of genes.
gene_set_name	The name of a gene set.
isNormalizedByHouseKeeping	is logical. If TRUE, the gene expression will be normalized by the expression of house keeping genes.
vertex.color1	The first color of gene expression gradient. Default blue
edge.size	The size of the edge. Default 0.2
edge.color	The edge color. Default gray
vertex.base.color	The node base color. Default gray35
background.color	The background color. Default white
vertext.size	The node size. Default 0.5
vertext.color2	The second color of gene expression gradient. Default red

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