plotClusteredTSNE: Plot t-SNE. Addtionally, it can highlight clusters or states.

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

Description

Plot t-SNE. Addtionally, it can highlight clusters or states.

Usage

plotClusteredTSNE(sceObject, dataDirectory, experimentName,
  tSNEresExp = "", colorPalette = "default", PCs = c(4, 6, 8, 10, 20,
  40, 50), perplexities = c(30, 40), columnName = "clusters",
  returnPlot = FALSE, width = 6, height = 5, ...)

Arguments

sceObject	a SingleCellExperiment object with your experiment.
dataDirectory	output directory for CONCLUS (supposed to be the same for one experiment during the workflow).
experimentName	name of the experiment which will appear in filenames (supposed to be the same for one experiment during the workflow).
tSNEresExp	if t-SNE coordinates were generated in a different CONCLUS run, you can use them without renaming the files. Please copy tsnes folder from the source run to the current one and write that experimentName in the tSNEresExp argument.
colorPalette	"default" or a vector of colors for the column "clusters" in the colData, for example c("yellow", "#CC79A7").
PCs	vector of PCs (will be specified in filenames).
perplexities	vector of perplexities (will be specified in filenames).
columnName	name of the column to plot on t-SNE dimensions.
returnPlot	boolean, return plot or not.
width	plot width.
height	plot height.
...	other arguments of the pdf() function.

Value

A ggplot object or nothing (depends on the returnPlot parameter).

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