Violin-Plot: Violin Plot

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

Violin Plot

Description

The "ViolinPlot" map makes plots to show gene expression patterns of the clusters or other factors. The default groups cells into the clusters, but the users can input the factor (column name) of coldata.

Usage

ViolinPlot(
  object,
  colFactor = NULL,
  genes = NULL,
  legend = TRUE,
  trim = TRUE,
  Colors = NULL,
  Alpha = 0.8,
  dots = TRUE,
  wid = "area"
)

Arguments

object	RISC object: a framework dataset.
colFactor	Use the factor (column name) in the coldata to make heatmap, but each time only one column name can be inputted.
genes	The gene expression pattern: gene symbol
legend	Whether a legend shown at heatmap.
trim	Whether trim the violin plot
Colors	The users can use their own colors (color vector). The default of the "UMAPlot" funciton will assign colors automatically.
Alpha	Whether show transparency of individual points, the default is 0.8.
dots	Adding jitter dots to the violin plot. The default is TRUE.
wid	The scale format, options: "area", "width", "count". The default: "area"

References

Wickham, H. (2016)

Auguie, B. (2015)

Examples

# RISC object
obj0 = raw.mat[[3]]
ViolinPlot(obj0, colFactor = 'Group', genes = 'Gene718')

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