plot_markers: Plot Cluster Marker Genes

In whtns/seuratTools: Tools for Managing Seurat Objects

Plot Cluster Marker Genes

Description

Plot a dot plot of n marker features grouped by cell metadata available methods are wilcoxon rank-sum test implemented in presto and specificity scores implemented in genesorteR

Usage

plot_markers(
  seu,
  metavar = "batch",
  num_markers = 5,
  selected_values = NULL,
  return_plotly = FALSE,
  marker_method = "presto",
  seurat_assay = "gene",
  hide_technical = NULL,
  unique_markers = FALSE,
  p_val_cutoff = 1,
  ...
)

Arguments

seu	a seurat object
metavar	the metadata variable from which to pick clusters
num_markers	default is 5
return_plotly	whether to return an interactive ploly plot
marker_method	either "presto" or "genesorteR"
hide_technical	whether to exclude mitochondrial or ribosomal genes
...

Examples

# interactive mode using "presto"
plot_markers(human_gene_transcript_seu, metavar = "tech", marker_method = "presto", return_plotly = TRUE)

# static mode using "presto"
plot_markers(human_gene_transcript_seu, metavar = "tech", marker_method = "genesorteR", return_plotly = FALSE)

whtns/seuratTools documentation built on Oct. 28, 2024, 7:18 a.m.