plotCellSimilarity: Save a cells similarity matrix.

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

Description

This function plots similarity matrix as a heatmap, so one can see similarity between parts of different clusters.

Usage

plotCellSimilarity(sceObject, cellsSimilarityMatrix, dataDirectory,
  experimentName, colorPalette = "default", statePalette = "default",
  clusteringMethod = "ward.D2", orderClusters = FALSE,
  plotPDF = TRUE, returnPlot = FALSE, width = 7, height = 6, ...)

Arguments

sceObject	a SingleCellExperiment object with your experiment.
cellsSimilarityMatrix	an output matrix from the conclus::clusterCellsInternal() function.
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).
colorPalette	"default" or a vector of colors for the column "clusters" in the colData, for example c("yellow", "#CC79A7").
statePalette	"default" or a vector of colors for the column "state" in the colData, for example c("yellow", "#CC79A7").
clusteringMethod	a clustering methods passed to hclust() function.
orderClusters	boolean, order clusters or not.
plotPDF	if TRUE export to pdf, if FALSE export to png. FALSE is recommended for datasets with more than 2500 cells due to large pdf file size.
returnPlot	boolean, return plot or not. Default if FALSE.
width	plot width.
height	plot height.
...	other parameters of pdf(), pheatmap() and png() functions.

Value

A ggplot object or nothing (depends on the returnPlot parameter). It saves the pdf in "dataDirectory/pictures" folder.

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