plotFreqHeatmap {CATALYST} | R Documentation

## Cluster frequency heatmap

### Description

Heatmap of relative cluster abundances (frequencies) by sample.

### Usage

    plotFreqHeatmap(
      x,
      k = "meta20",
      m = NULL,
      normalize = TRUE,
      row_anno = TRUE,
      col_anno = TRUE,
      row_clust = TRUE,
      col_clust = TRUE,
      row_dend = TRUE,
      col_dend = TRUE,
      bars = TRUE,
      perc = FALSE,
      hm_pal = rev(brewer.pal(11, "RdBu")),
      k_pal = CATALYST:::.cluster_cols,
      m_pal = k_pal
    )

### Arguments

`x` | a `SingleCellExperiment`.
`k` | character string specifying the clustering to use; valid values are `names(cluster_codes(x))`. Cell counts will be computed across these cluster IDs.
`m` | character string specifying a metaclustering to include as an annotation when `row_anno = TRUE`.
`normalize` | logical specifying whether to Z-score normalize.
`row_anno, col_anno` | logical specifying whether to include row/column annotations for clusters/samples; for `col_anno`, this can be a character vector specifying a subset of `names(colData(x))` to be included.
`row_clust, col_clust` | logical specifying whether rows/columns (clusters/samples) should be hierarchically clustered and re-ordered accordingly.
`row_dend, col_dend` | logical specifying whether to include row/column dendrograms.
`bars` | logical specifying whether to include a barplot of cell counts per cluster as a right-hand side row annotation.
`perc` | logical specifying whether to display percentage labels next to bars when `bars = TRUE`.
`hm_pal` | character vector of colors to interpolate for the heatmap.
`k_pal, m_pal` | character vector of colors to use for cluster and merging row annotations. If less than `nlevels(cluster_ids(x, k/m))` values are supplied, colors will be interpolated via `colorRampPalette`.

### Value

a `Heatmap-class` object.

### Author(s)

Helena L Crowell helena.crowell@uzh.ch

### See Also

`plotAbundances`, `plotExprHeatmap`, `plotMultiHeatmap`,

### Examples

    data(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- cluster(sce)

    # complete
    plotFreqHeatmap(sce, k = "meta12", m = "meta8")

    # minimal
    plotFreqHeatmap(sce, k = "meta10",
      normalize = FALSE, bars = FALSE,
      row_anno = FALSE, col_anno = FALSE,
      row_clust = FALSE, col_clust = FALSE)

    # customize colors & annotations
    plotFreqHeatmap(sce,
      k = "meta7", m = "meta4",
      col_anno = "condition",
      hm_pal = c("navy", "grey95", "gold"),
      k_pal = hcl.colors(7, "Set 2"),
      m_pal = hcl.colors(4, "Dark 3"))

[Package CATALYST version 1.14.1 Index]