plotCellHeatmap: Save markers heatmap.

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

Description

This function plots heatmap with marker genes on rows and clustered cells on columns.

Usage

plotCellHeatmap(markersClusters, sceObject, dataDirectory, experimentName,
  fileName, meanCentered = TRUE, colorPalette = "default",
  statePalette = "default", clusteringMethod = "ward.D2",
  orderClusters = FALSE, orderGenes = FALSE, returnPlot = FALSE,
  saveHeatmapTable = FALSE, width = 10, height = 8.5, ...)

Arguments

markersClusters	a data frame where the first column is "geneName" containing genes names from sceObject, and the second column is corresponding "clusters". All names from that column must come from the column "clusters" in the colData(sceObject). The data frame can be obtained from conclus::getMarkerGenes() function or created manually.
sceObject	a SingleCellExperiment object with your experiment.
dataDirectory	output directory of a given CONCLUS run (supposed to be the same for one experiment during the workflow).
experimentName	name of the experiment which appears in filenames (supposed to be the same for one experiment during the workflow).
fileName	name of the ouput file
meanCentered	boolean, should mean centering be applied to the expression data or not.
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, should the heatmap be structured by clusters.
orderGenes	boolean, should the heatmap be structured by genes.
returnPlot	boolean, whether to return a ggplot object with the plot or not.
saveHeatmapTable	boolean, whether to save the expression matrix used for heatmap into a .csv file or not. The file will be saved into 'dataDirectory/output_tables' with the same name as the .pdf plot.
width	plot width.
height	plot height.
...	other parameters from pdf() and pheatmap() functions.

Value

A ggplot object of the plot if needed. The function saves pdf in "dataDirectiry/pictures" folder.

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