plotViolin: This will create a violin plot

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This will plot a given gene via violin plot

Usage

plotViolin(
  gene,
  input,
  sampleID,
  colourID,
  facetID = NULL,
  cols = NULL,
  subsetID = NA,
  subsetName = NA,
  facet_scale = "fixed",
  mean_text = F,
  fraction_text = F,
  type = "violin",
  legend = T,
  fudge = 0
)

Arguments

gene	Will only plot data for this gene, if the gene paramter is a list the violin plot will display the sum of the expression for all genes in the list
input	Input expression set
sampleID	pData variable to group by on the x axis
colourID	a pData variable to color by
facetID	an optional pData variable to plot by
cols	Personalized colour vector, length should equal number of groups in colourID
subsetID	a pData variable to subset the original data by
subsetName	a value from the subsetID variable specified, this will select only these cells to plot
facet_scale	ggplot2 parameter for plot scales defaults to fixed
mean_text	ggplot2 parameter for adding the mean expression per group defaults to False
fraction_text	ggplot2 parameter for adding the fraction of cells with expression greater than 0 for that gene defaults to False
type	plot type, default is violin, can also plot density and cdf distribution
fudge	a pseudocount value to avoid dropping cells with zero counts

Details

Utilize information stored in pData to control the plot display.

Examples

plotViolin("Actb", input, sampleID = "sample", facetID = "subtype", colourID = "genotype", cols = NULL, subsetID = "celltype", subsetName = "Neurons", facet_scale = "fixed")

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.