scScoreDimPlot: scScoreDimPlot

In ncrna/Yeskit: Yet Another Single-Cell Analysis Toolkit (Yeskit)

scScoreDimPlot

Description

MSigdb scoring DimPlot for single-cell clusters

Usage

scScoreDimPlot(
  object = NULL,
  signature = NULL,
  reduction = NULL,
  cols = NULL,
  pt.size = NULL,
  split.by = NULL,
  title = NULL,
  ncol = NULL,
  raster = TRUE,
  scale = TRUE,
  col.min = NA,
  col.max = NA
)

Arguments

object	Seurat object
signature	Name of one gene set
reduction	Which dimensionality reduction to use
cols	Colors to plot
pt.size	Adjust point size to plot, default pt.size=0.5
split.by	Name of a metadata column to split plot by
title	Title of the plot
ncol	Number of columns for display the plots
raster	Convert points to raster format, default is TRUE
scale	Determine whether to scale the data, default is TRUE
col.min	Minimum scaled average score threshold (smaller values will be set to this)
col.max	Maximum scaled average score threshold (larger values will be set to this)

Value

A ggplot object

Examples

data("H3N2_small")
scScoreDimPlot(object = H3N2_small,
  signature = "HALLMARK_INFLAMMATORY_RESPONSE",
  reduction = "umap",
  cols = NULL,
  split.by = "sample",
  ncol = 2,
  pt.size = 1 
)

ncrna/Yeskit documentation built on Nov. 4, 2024, 10:32 p.m.