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]