plot_umap_label_by_AUCell_score: Plot UMAP with AUCell score

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

Plot UMAP with AUCell score

Description

Plot UMAP with AUCell score

Usage

plot_umap_label_by_AUCell_score(
  object,
  AUCell_gene_set_name = c(),
  AUCell_score,
  AUCell_cutoff = 0,
  IsShowOnlySampleIDs = FALSE,
  selected.sampleID = c(),
  IsDownsample = F,
  downsample.size = 0,
  IsLimitedAUCscoreByClusters = FALSE,
  selected.limited.clusters = c(),
  clustering_method = "louvain",
  point.size = 1,
  point.color1 = "black",
  point.color2 = "red",
  showLegend = 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.
IsDownsample	is logical. If TRUE, only downsampled cells will be displayed.
downsample.size	is the downsample size. Default 0
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.
point.size	The point size. Default 1
point.color1	The color for a low AUCell score. Default gray
point.color2	The color for a high AUCell score . Default red

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