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 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. |
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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