plotClusterHeatmap: Plot cluster heatmap

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Plot cluster heatmap

Description

Plots expression & relative cluster abundances heatmaps summarizing a clustering and/or metaclustering.

Usage

plotClusterHeatmap(
  x,
  hm2 = NULL,
  k = "meta20",
  m = NULL,
  fun = c("median", "mean"),
  cluster_anno = TRUE,
  split_by = NULL,
  scale = TRUE,
  draw_dend = TRUE,
  draw_freqs = FALSE,
  palette = rev(brewer.pal(11, "RdYlBu"))
)

Arguments

x	a SingleCellExperiment.
hm2	character string. Specifies the right-hand side heatmap. One of: "abundances": cluster frequencies across samples "state": median cell state marker expressions across clusters (analogous to the left-hand side heatmap) a character string/vector corresponding to one/multiple marker(s): aggregated marker expressions across samples and clusters
k	character string specifying the clustering across which median marker expressions should be computed.
m	character string specifying the metaclustering to be shown. (This is for display only and will not effect any computations!)
fun	character string specifying the function to use as summary statistic.
cluster_anno	logical specifying if clusters should be annotated.
split_by	deprecated.
scale	logical specifying whether scaled values should be plotted.
draw_dend	logical specifying if the row dendrogram should be drawn.
draw_freqs	logical specifying whether to display cell counts and proportions.
palette	character vector of colors to interpolate.

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.

In its 1st panel, plotClusterHeatmap will display median (scaled, arcsinh-transformed) cell-type marker expressions (across all samples). Depending on argument hm2, the 2nd panel will contain one of:

• relataive cluster abundances by sample

• median (scaled, arcsinh-transformed) cell-state marker expressions (across all samples)

• median (scaled, arcsinh-transformed) cell-state marker expressions by sample

Value

a HeatmapList-class object.

Author(s)

Helena Lucia Crowell [e-mail]

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)

HelenaLC/CATALYST documentation built on April 1, 2024, 3:16 a.m.