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, 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 daFrame.

...

optional arguments.

bin_anno

logical. Specifies whether to display values insinde each bin.

row_anno

logical. Should row annotations for each factor in metadata(x) be included?

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], draw_freqs=TRUE)


[Package CATALYST version 1.8.4 Index]