plotFreqHeatmap: Cluster frequency heatmap

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Cluster frequency heatmap

Description

Heatmap of relative cluster abundances (frequencies) by sample.

Usage

plotFreqHeatmap(
  x,
  k = "meta20",
  m = NULL,
  normalize = TRUE,
  row_anno = TRUE,
  col_anno = TRUE,
  row_clust = TRUE,
  col_clust = TRUE,
  row_dend = TRUE,
  col_dend = TRUE,
  bars = TRUE,
  perc = FALSE,
  hm_pal = rev(brewer.pal(11, "RdBu")),
  k_pal = .cluster_cols,
  m_pal = k_pal
)

Arguments

x	a SingleCellExperiment.
k	character string specifying the clustering to use; valid values are names(cluster_codes(x)). Cell counts will be computed across these cluster IDs.
m	character string specifying a metaclustering to include as an annotation when row_anno = TRUE.
normalize	logical specifying whether to Z-score normalize.
row_anno, col_anno	logical specifying whether to include row/column annotations for clusters/samples; for col_anno, this can be a character vector specifying a subset of names(colData(x)) to be included.
row_clust, col_clust	logical specifying whether rows/columns (clusters/samples) should be hierarchically clustered and re-ordered accordingly.
row_dend, col_dend	logical specifying whether to include row/column dendrograms.
bars	logical specifying whether to include a barplot of cell counts per cluster as a right-hand side row annotation.
perc	logical specifying whether to display percentage labels next to bars when bars = TRUE.
hm_pal	character vector of colors to interpolate for the heatmap.
k_pal, m_pal	character vector of colors to use for cluster and merging row annotations. If less than nlevels(cluster_ids(x, k/m)) values are supplied, colors will be interpolated via colorRampPalette.

Value

a Heatmap-class object.

Author(s)

Helena L Crowell [e-mail]

See Also

plotAbundances, plotExprHeatmap, plotMultiHeatmap,

Examples

data(PBMC_fs, PBMC_panel, PBMC_md)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
sce <- cluster(sce)

# complete 
plotFreqHeatmap(sce, k = "meta12", m = "meta8")

# minimal 
plotFreqHeatmap(sce, k = "meta10",
  normalize = FALSE, bars = FALSE,
  row_anno = FALSE, col_anno = FALSE,
  row_clust = FALSE, col_clust = FALSE)
  
# customize colors & annotations
plotFreqHeatmap(sce, 
  k = "meta7", m = "meta4",
  col_anno = "condition",
  hm_pal = c("navy", "grey95", "gold"),
  k_pal = hcl.colors(7, "Set 2"),
  m_pal = hcl.colors(4, "Dark 3"))

HelenaLC/CATALYST documentation built on Oct. 16, 2024, 12:21 a.m.