plotDEheatmap: Plot a heatmap of differential genes

In conos: Clustering on Network of Samples

Plot a heatmap of differential genes

Description

Plot a heatmap of differential genes

Usage

plotDEheatmap(
  con,
  groups,
  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 = 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,
  max.cells = Inf,
  ...
)

Arguments

con	conos (or p2) object
groups	groups in which the DE genes were determined (so that the cells can be ordered correctly)
de	differential expression result (list of data frames) (default=NULL)
min.auc	optional minimum AUC threshold (default=NULL)
min.specificity	optional minimum specificity threshold (default=NULL)
min.precision	optional minimum precision threshold (default=NULL)
n.genes.per.cluster	numeric Number of genes to show for each cluster (default=10)
additional.genes	optional additional genes to include (the genes will be assigned to the closest cluster) (default=NULL)
exclude.genes	an optional list of genes to exclude from the heatmap (default=NULL)
labeled.gene.subset	a subset of gene names to show (instead of all genes) (default=NULL). Can be a vector of gene names, or a number of top genes (in each cluster) to show the names for.
expression.quantile	numeric Expression quantile to show (default=0.99)
pal	palette to use for the main heatmap (default=colorRampPalette(c('dodgerblue1','grey95','indianred1'))(1024))
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 (default=NULL).
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	boolean Whether to show the cluster legend (default=TRUE)
show_heatmap_legend	boolean Whether to show the expression heatmap legend (default=FALSE)
border	boolean Whether to show borders around the heatmap and annotations (default=TRUE)
return.details	boolean 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 (default=FALSE).
row.label.font.size	numeric Font size for the row labels (default=10)
order.clusters	boolean Whether to re-order the clusters according to the similarity of the expression patterns (of the genes being shown) (default=FALSE)
split	boolean Whether to use arguments "row_split" and "column_split" in ComplexHeatmap::Heatmap() (default=FALSE). These arguments are categorical vectors used to split the rows/columns in the heatmap.
split.gap	numeric Value of millimeters "mm" to use for 'row_gap' and 'column_gap' (default=0). If split is FALSE, this argument is ignored.
cell.order	explicitly supply cell order (default=NULL)
averaging.window	numeric Optional window averaging between neighboring cells within each group (turned off by default) - useful when very large number of cells shown (requires zoo package) (default=0)
max.cells	numeric Maximum cells to include in any given group (default: Inf)
...	extra parameters are passed to ComplexHeatmap::Heatmap() call

Value

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

conos documentation built on May 29, 2024, 9:56 a.m.