plotDEheatmap_conos: 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,
  ...
)

Value

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

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