plot_forceDirectedGraph_label_by_AUCell_score: Plot force-direct graph with AUCell score

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

Plot force-direct graph with AUCell score

Description

Plot force-direct graph with AUCell score

Usage

plot_forceDirectedGraph_label_by_AUCell_score(
  object,
  AUCell_gene_set_name = c(),
  AUCell_score,
  AUCell_cutoff = 0,
  IsShowOnlySampleIDs = FALSE,
  selected.sampleID = c(),
  IsLimitedAUCscoreByClusters = FALSE,
  selected.limited.clusters = c(),
  clustering_method = "louvain",
  vertex.size = 1.5,
  edge.size = 0.2,
  vertex.color1 = "black",
  vertex.color2 = "red",
  edge.color = "gray",
  background.color = "white",
  showEdge = T
)

Arguments

object	The SingCellaR object.
AUCell_gene_set_name	The vector of gene set names.
AUCell_score	The dataframe of AUCell score per gene set.
AUCell_cutoff	The cutoff score. Default 0
IsShowOnlySampleIDs	is logical. If TRUE, only selected sample IDs will be shown.
selected.sampleID	The selected sample IDs.
IsLimitedAUCscoreByClusters	is logical. If TRUE, AUCell score will be limited by selected clusters.
selected.limited.clusters	The selected clusters of interest.
clustering_method	The clustering method.
vertex.size	The node size. Default 1.5
edge.size	The edge size. Default 0.2
vertex.color1	The color for a low AUCell score. Default black
vertex.color2	The color for a high AUCell score. Default red
edge.color	The edge color.
background.color	The background color.
showEdge	is logical. If TRUE, the edge will be displayed.

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