plotClustersSimilarity: Save a similarity cluster matrix.

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

Description

Save a similarity cluster matrix.

Usage

plotClustersSimilarity(clustersSimilarityMatrix, sceObject, dataDirectory,
  experimentName, colorPalette, statePalette, clusteringMethod,
  returnPlot = FALSE, width = 7, height = 5.5, ...)

Arguments

clustersSimilarityMatrix	a matrix, result of conclus::calculateClustersSimilarity() function.
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).
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.
returnPlot	boolean, return plot or not.
width	plot width.
height	plot height.
...	other parameters of pdf() and pheatmap() functions.

Value

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

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