UMAPlot: UMAP Plots

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

UMAP Plots

Description

The UMAP plots are widespread in scRNA-seq data analysis. Here, the "UMAPlot" function not only can make plots for factor labels of individual cells but also can show gene expression values of each cell.

Usage

UMAPlot(
  object,
  colFactor = NULL,
  genes = NULL,
  legend = TRUE,
  Colors = NULL,
  size = 0.5,
  Alpha = 0.8,
  plot.ncol = NULL,
  raw.count = FALSE,
  exp.range = NULL,
  exp.col = "firebrick2"
)

Arguments

object	RISC object: a framework dataset.
colFactor	Use the factor (column name) in the coldata to make a UMAP plot, but each time only one column name can be inputted.
genes	Use the gene expression values (gene symbol) to make UMAP plots, each time more than one genes can be inputted.
legend	Whether a legend shown at UMAP plot.
Colors	The users can use their own colors (color vector). The default of the "UMAPlot" funciton will assign colors automatically.
size	Choose the size of dots at UMAP plots, the default size is 0.5.
Alpha	Whether show transparency of individual points, the default is 0.8.
plot.ncol	If the users input more than one genes, the arrangement of multiple UMAP plots depends on this parameter.
raw.count	If use normalized or raw counts.
exp.range	The gene expression cutoff for plot, e.g. "c(0, 1.5)" for expression level between 0 and 1.5.
exp.col	The gradient color for gene expression.

References

Wickham, H. (2016)

Auguie, B. (2015)

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.