plotExprHeatmap {CATALYST} | R Documentation

## Plot expression heatmap

### Description

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

### Usage

    plotExprHeatmap(x, ...)

    ## S4 method for signature 'daFrame'
    plotExprHeatmap(x, anno = TRUE, color_by = NULL,
      palette = brewer.pal(n = 8, name = "YlGnBu"), scale = TRUE,
      draw_freqs = FALSE, clustering_distance = "euclidean",
      clustering_linkage = "average")

### Arguments

`x` | a `daFrame`.
`...` | optional arguments.
`anno` | logical. Specifies whether to display values insinde each bin.
`color_by` | character string. Specifies the row annotation.
`palette` | character vector of colors to interpolate.
`scale` | logical. Specifies whether scaled values should be displayed. (see below for details)
`draw_freqs` | logical. Specifyies whether to display cell counts and proportions.
`clustering_distance` | a character string that specifies the metric to use in `dist()` for clustering.
`clustering_linkage` | a 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)
    daf <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)
    plotExprHeatmap(daf[, 1:5], color_by="condition", draw_freqs=TRUE)

[Package CATALYST version 1.6.7 Index]