celdaProbabilityMap {celda} | R Documentation |
Renders probability and relative expression heatmaps to visualize the relationship between features and cell populations (or cell populations and samples).
celdaProbabilityMap( sce, useAssay = "counts", altExpName = "featureSubset", level = c("cellPopulation", "sample"), ncols = 100, col2 = circlize::colorRamp2(c(-2, 0, 2), c("#1E90FF", "#FFFFFF", "#CD2626")), title1 = "Absolute probability", title2 = "Relative expression", showColumnNames = TRUE, showRowNames = TRUE, rowNamesgp = grid::gpar(fontsize = 8), colNamesgp = grid::gpar(fontsize = 12), clusterRows = FALSE, clusterColumns = FALSE, showHeatmapLegend = TRUE, heatmapLegendParam = list(title = NULL, legend_height = grid::unit(6, "cm")), ... ) ## S4 method for signature 'SingleCellExperiment' celdaProbabilityMap( sce, useAssay = "counts", altExpName = "featureSubset", level = c("cellPopulation", "sample"), ncols = 100, col2 = circlize::colorRamp2(c(-2, 0, 2), c("#1E90FF", "#FFFFFF", "#CD2626")), title1 = "Absolute probability", title2 = "Relative expression", showColumnNames = TRUE, showRowNames = TRUE, rowNamesgp = grid::gpar(fontsize = 8), colNamesgp = grid::gpar(fontsize = 12), clusterRows = FALSE, clusterColumns = FALSE, showHeatmapLegend = TRUE, heatmapLegendParam = list(title = NULL, legend_height = grid::unit(6, "cm")), ... )
sce |
A SingleCellExperiment object returned by celda_C, celda_G, or celda_CG. |
useAssay |
A string specifying which assay slot to use. Default "counts". |
altExpName |
The name for the altExp slot to use. Default "featureSubset". |
level |
Character. One of "cellPopulation" or "Sample".
"cellPopulation" will display the absolute probabilities and relative
normalized expression of each module in each cell population.
|
ncols |
The number of colors (>1) to be in the color palette of the absolute probability heatmap. |
col2 |
Passed to |
title1 |
Passed to |
title2 |
Passed to |
showColumnNames |
Passed to |
showRowNames |
Passed to |
rowNamesgp |
Passed to |
colNamesgp |
Passed to |
clusterRows |
Passed to |
clusterColumns |
Passed to |
showHeatmapLegend |
Passed to |
heatmapLegendParam |
Passed to |
... |
Additional parameters passed to Heatmap. |
A HeatmapList object containing 2 Heatmap-class objects
celda_C for clustering cells. celda_CG for clustering features and cells
data(sceCeldaCG) celdaProbabilityMap(sceCeldaCG)