plotGeneExpression: plotGeneExpression

In PolinaPavlovich/CONCLUS: ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.

Description

The function saves a t-SNE plot colored by expression of a given gene. Warning: filename with t-SNE results is hardcoded, so please don't rename the output file.

Usage

plotGeneExpression(geneName, experimentName, dataDirectory,
  graphsDirectory = "pictures", sceObject, tSNEpicture = 1,
  commentName = "", palette = c("grey", "red", "#7a0f09", "black"),
  returnPlot = FALSE, savePlot = TRUE, alpha = 1, limits = NA,
  pointSize = 1, width = 6, height = 5, ...)

Arguments

geneName	name of the gene you want to plot.
experimentName	name of the experiment which appears in filenames (supposed to be the same for one experiment during the workflow).
dataDirectory	output directory for CONCLUS (supposed to be the same for one experiment during the workflow).
graphsDirectory	name of the subdirectory where to put graphs. Default is "dataDirectory/pictures".
sceObject	a SingleCellExperiment object with your experiment.
tSNEpicture	number of the picture you want to use for plotting. Please check "dataDirectory/tsnes" or "dataDirectory/pictures/tSNE_pictures/clusters" to get the number, it is usually from 1 to 14.
commentName	comment you want to specify in the filename.
palette	color palette for the legend.
returnPlot	boolean, should the function return a ggplot object or not.
savePlot	boolean, should the function export the plot to pdf or not.
alpha	opacity of the points of the plot.
limits	range of the gene expression shown in the legend. This option allows generating t-SNE plots with equal color scale to compare the expression of different genes. By default, limits are the range of expression of a selected gene.
pointSize	size of the point.
width	plot width.
height	plot height.
...	other parameters of the pdf() function.

Value

A ggplot object of the plot if needed.

PolinaPavlovich/CONCLUS documentation built on May 10, 2019, 2:42 p.m.