plotDEheatmap_conos: Plot a heatmap of differential genes. Code is adapted from...

In scITD: Single-Cell Interpretable Tensor Decomposition

Plot a heatmap of differential genes. Code is adapted from Conos package. https://github.com/kharchenkolab/conos/blob/master/R/plot.R

Description

Plot a heatmap of differential genes. Code is adapted from Conos package. https://github.com/kharchenkolab/conos/blob/master/R/plot.R

Usage

plotDEheatmap_conos(
  con,
  groups,
  container,
  de = NULL,
  min.auc = NULL,
  min.specificity = NULL,
  min.precision = NULL,
  n.genes.per.cluster = 10,
  additional.genes = NULL,
  exclude.genes = NULL,
  labeled.gene.subset = NULL,
  expression.quantile = 0.99,
  pal = (grDevices::colorRampPalette(c("dodgerblue1", "grey95", "indianred1")))(1024),
  ordering = "-AUC",
  column.metadata = NULL,
  show.gene.clusters = TRUE,
  remove.duplicates = TRUE,
  column.metadata.colors = NULL,
  show.cluster.legend = TRUE,
  show_heatmap_legend = FALSE,
  border = TRUE,
  return.details = FALSE,
  row.label.font.size = 10,
  order.clusters = FALSE,
  split = FALSE,
  split.gap = 0,
  cell.order = NULL,
  averaging.window = 0,
  ...
)

Arguments

con	conos (or p2) object
groups	groups in which the DE genes were determined (so that the cells can be ordered correctly)
container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
de	differential expression result (list of data frames)
min.auc	optional minimum AUC threshold
min.specificity	optional minimum specificity threshold
min.precision	optional minimum precision threshold
n.genes.per.cluster	number of genes to show for each cluster
additional.genes	optional additional genes to include (the genes will be assigned to the closest cluster)
exclude.genes	an optional list of genes to exclude from the heatmap
labeled.gene.subset	a subset of gene names to show (instead of all genes). Can be a vector of gene names, or a number of top genes (in each cluster) to show the names for.
expression.quantile	expression quantile to show (0.98 by default)
pal	palette to use for the main heatmap
ordering	order by which the top DE genes (to be shown) are determined (default "-AUC")
column.metadata	additional column metadata, passed either as a data.frame with rows named as cells, or as a list of named cell factors.
show.gene.clusters	whether to show gene cluster color codes
remove.duplicates	remove duplicated genes (leaving them in just one of the clusters)
column.metadata.colors	a list of color specifications for additional column metadata, specified according to the HeatmapMetadata format. Use "clusters" slot to specify cluster colors.
show.cluster.legend	whether to show the cluster legend
show_heatmap_legend	whether to show the expression heatmap legend
border	show borders around the heatmap and annotations
return.details	if TRUE will return a list containing the heatmap (ha), but also raw matrix (x), expression list (expl) and other info to produce the heatmap on your own.
row.label.font.size	font size for the row labels
order.clusters	whether to re-order the clusters according to the similarity of the expression patterns (of the genes being shown)
split	logical If TRUE splits the heatmap by cell type (default=FALSE)
split.gap	numeric The distance to put in the gaps between split parts of the heatmap if split=TRUE (default=0)
cell.order	explicitly supply cell order
averaging.window	optional window averaging between neighboring cells within each group (turned off by default) - useful when very large number of cells shown (requires zoo package)
...	extra parameters are passed to pheatmap

Value

ComplexHeatmap::Heatmap object (see return.details param for other output)

scITD documentation built on Sept. 8, 2023, 5:11 p.m.