plotClusterHeatmap: Plot cluster heatmap

In casanova-lab/iMUBAC: Integration of Multi-Batch Cytometry datasets

Plot cluster heatmap

Description

Heatmaps summarizing the clustering result.

Usage

plotClusterHeatmap(
  sce,
  features = rownames(sce),
  clusters = sce$cluster_id,
  by_exprs_values = "exprs",
  fun = "median",
  scale = T,
  cluster_rows = T,
  cluster_anno = F,
  draw_dend = T,
  draw_freqs = T,
  split_by = NULL,
  hm2 = NULL
)

Arguments

sce	A SingleCellExperiment object.
features	A character vector. Specifies which antigens to use for clustering.
clusters	A character vector. Specifies the cluster IDs.
by_exprs_values	A character string. Specifies which assay data to use for plotting.
fun	A character string. Specifies the function for computing the summary statistic.
scale	Logical. Specifies whether scaled values should be plotted. Scaled values corresponds to cofactor arcsinh-transformed expression values scaled between 0 and 1 using 1 Note that hierarchical clustering is performed on the unscaled data.
cluster_rows	Logical. Specifies whether rows should be reordered by hierarchical clustering.
cluster_anno	Logical. Specifies whether clusters should be annotated.
draw_dend	Logical. Specifies if the row dendrogram should be drawn.
draw_freqs	Logical. Specifyies whether to display cell counts and proportions.
split_by	A character string. Must corresponds to a column name of rowData(sce). If specified, the data will be subset according to this variable, and multiple heatmaps will be drawn.
hm2	A character string. Specifies the right-hand side heatmap. One of: "abundances": cluster frequencies across samples a character string/vector corresponding to one/multiple marker(s): median marker expressions across samples and clusters Depending on argument hm2, the side heatmap can contain one of: relataive cluster abundances by sample median (scaled, arcsinh-transformed) marker expressions by sample

Value

a HeatmapList-class object.

casanova-lab/iMUBAC documentation built on Sept. 13, 2022, 6:36 p.m.