Description Usage Arguments Value
This function plots similarity matrix as a heatmap, so one can see similarity between parts of different clusters.
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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. |
A ggplot object or nothing (depends on the returnPlot parameter). It saves the pdf in "dataDirectory/pictures" folder.
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