plotDEheatmap {conos}R Documentation

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)


[Package conos version 1.4.2 Index]