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]