plotClusterHeatmap {CATALYST} | R Documentation

## Plot cluster heatmap

### Description

Plots expression & relative cluster abundances heatmaps summarizing a clustering and/or metaclustering.

### Usage

    plotClusterHeatmap(
      x,
      hm2 = NULL,
      k = "meta20",
      m = NULL,
      fun = c("median", "mean"),
      cluster_anno = TRUE,
      split_by = NULL,
      scale = TRUE,
      draw_dend = TRUE,
      draw_freqs = FALSE,
      palette = rev(brewer.pal(11, "RdYlBu"))
    )

### Arguments

`x` | a `SingleCellExperiment`.
`hm2` | character string. Specifies the right-hand side heatmap. One of: `"abundances"`: cluster frequencies across samples `"state"`: median cell state marker expressions across clusters (analogous to the left-hand side heatmap) a character string/vector corresponding to one/multiple marker(s): aggregated marker expressions across samples and clusters
`k` | character string specifying the clustering across which median marker expressions should be computed.
`m` | character string specifying the metaclustering to be shown. (This is for display only and will not effect any computations!)
`fun` | character string specifying the function to use as summary statistic.
`cluster_anno` | logical specifying if clusters should be annotated.
`split_by` | deprecated.
`scale` | logical specifying whether scaled values should be plotted.
`draw_dend` | logical specifying if the row dendrogram should be drawn.
`draw_freqs` | logical specifying whether to display cell counts and proportions.
`palette` | character vector of colors to interpolate.

### Details

Scaled values corresponds to cofactor arcsinh-transformed expression values scaled between 0 and 1 using 1 boundaries. Hierarchical clustering is performed on the unscaled data.

In its 1st panel, `plotClusterHeatmap` will display median (scaled, arcsinh-transformed) cell-type marker expressions (across all samples). Depending on argument `hm2`, the 2nd panel will contain one of:

- relataive cluster abundances by sample

- median (scaled, arcsinh-transformed) cell-state marker expressions (across all samples)

- median (scaled, arcsinh-transformed) cell-state marker expressions by sample

### Value

a `HeatmapList-class` object.

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

### References

Nowicka M, Krieg C, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

[Package CATALYST version 1.16.2 Index]