plotDEheatmap: 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,
  ...
)

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)
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