plotExprHeatmap {CATALYST} | R Documentation

## Plot expression heatmap

### Description

Plots median marker expressions across samples computed on arcsinh-transformed intensities.

### Usage

    plotExprHeatmap(
      x,
      bin_anno = TRUE,
      row_anno = TRUE,
      palette = brewer.pal(n = 8, name = "YlGnBu"),
      scale = TRUE,
      draw_freqs = FALSE,
      clustering_distance = "euclidean",
      clustering_linkage = "average"
    )

### Arguments

`x` | a `SingleCellExperiment`.
`bin_anno` | logical. Specifies whether to display values inside bins.
`row_anno` | logical. Should row annotations for each factor in `metadata(x)$experiment_info` be included?
`palette` | character vector of colors to interpolate.
`scale` | logical. Should scaled values be displayed? (see details)
`draw_freqs` | logical. Should cell counts and proportions be displayed?
`clustering_distance` | character string that specifies the metric to use in `dist` for clustering.
`clustering_linkage` | character string that specifies the linkage to use in `hclust` for clustering.

### 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.

### 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)

### Examples

    data(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    plotExprHeatmap(sce, draw_freqs=TRUE)

[Package CATALYST version 1.10.3 Index]