Plot an heatmap of feature values in cell clusters

Usage

plot_heatmap_features_by_clusters(
  scMuffinList = NULL,
  feature_source = NULL,
  partition_id = NULL,
  significance_matrix = NULL,
  sig_threshold = 0.05,
  file = NULL,
  width = 180,
  height = 180,
  units = "mm",
  res = 300,
  scale = FALSE,
  pal = NULL,
  na_col = "black",
  X_abs_max = NULL,
  ...
)

Arguments

scMuffinList: scMuffinList object
feature_source: It can be a "mean", "gss" or a numeric matrix (clusters-by-features). If "mean", the data.frame with average feature values among clusters will be used (default); if "gene_set_scoring", the average gene set values among clusters will be used.
partition_id: identifier of the partition to be considered
significance_matrix: optional significance matrix (clusters-by-features) of the same size of the data specified by means of feature_source
sig_threshold: significance threshold
file: File name to save the figure as png file
width: image width
height: image height
units: image units
res: image resolution
scale: whether to scale the features
pal: color palette. Default to rev(pals::brewer.rdylbu(10)) (negative values) or pals::brewer.ylorrd(5)) (positive values)
na_col: color for NA values
X_abs_max: maximum absolute value permitted, useful to avoid the effect of outliers over colors
...: further arguments to ComplexHeatmap::Heatmap