celdaProbabilityMap {celda} | R Documentation

## Probability map for a celda model

### Description

Renders probability and relative expression heatmaps to visualize the relationship between features and cell populations (or cell populations and samples).

### Usage

    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")),
      ...
    )

### Arguments

`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. `level = "cellPopulation"` only works for celda_CG `sce` objects. "sample" will display the absolute probabilities and relative normalized abundance of each cell population in each sample. Default "cellPopulation".
`ncols` | The number of colors (>1) to be in the color palette of the absolute probability heatmap.
`col2` | Passed to `col` argument of Heatmap. Set color boundaries and colors for the relative expression heatmap.
`title1` | Passed to `column_title` argument of Heatmap. Figure title for the absolute probability heatmap.
`title2` | Passed to `column_title` argument of Heatmap. Figure title for the relative expression heatmap.
`showColumnNames` | Passed to `show_column_names` argument of Heatmap. Show column names.
`showRowNames` | Passed to `show_row_names` argument of Heatmap. Show row names.
`rowNamesgp` | Passed to `row_names_gp` argument of Heatmap. Set row name font.
`colNamesgp` | Passed to `column_names_gp` argument of Heatmap. Set column name font.
`clusterRows` | Passed to `cluster_rows` argument of Heatmap. Cluster rows.
`clusterColumns` | Passed to `cluster_columns` argument of Heatmap. Cluster columns.
`showHeatmapLegend` | Passed to `show_heatmap_legend` argument of Heatmap. Show heatmap legend.
`heatmapLegendParam` | Passed to `heatmap_legend_param` argument of Heatmap. Heatmap legend parameters.
`...` | Additional parameters passed to Heatmap.

### Value

A HeatmapList object containing 2 Heatmap-class objects

### See Also

celda_C for clustering cells. celda_CG for clustering features and cells

### Examples

    data(sceCeldaCG)
    celdaProbabilityMap(sceCeldaCG)

[Package celda version 1.8.1 Index]