heatmapPlot: Generate Heatmap

In stevexniu/scMatchmaker: Single Cell Matchmaker

Generate Heatmap

Description

Generate a heatmap plot.

Usage

heatmapPlot(
  data,
  which.cell = NULL,
  which.gene = NULL,
  aggregate = c("none", "row", "column"),
  counted = FALSE,
  color = "RdBu",
  color.bins = 7,
  order = TRUE,
  order.dist = "minkowski",
  p = 1,
  filter = FALSE,
  low.cutoff = -Inf,
  high.cutoff = Inf,
  return.data = FALSE,
  Rowv = NA,
  Colv = NA,
  trace = "none",
  margins = c(10, 10),
  na.color = "black",
  key = TRUE,
  show.text = TRUE,
  ...
)

Arguments

data	Data matrix to plot
which.cell	Interacting cell type name or index to plot. Default is NULL.
which.gene	Interacting gene name or index to plot. Default is NULL.
aggregate	Type of aggregation used. row, aggregated by row (Default). column, aggregated by column none, no aggregation.
counted	Aggregate interactions counts instead of strengths. Default is FALSE.
color	Color palette name. Default is "RdBu", high values are in red and low values in blue. See details brewer.pal.
color.bins	Number of differen colors in pallete. Default is 7. See detail brewer.pal.
order	Whether to order the input data. Default is TRUE. See details seriate.
order.dist	Distance measure to be used. Default is "minkowski". See details dist.
p	Power of Minkowski distance Default is 1, aka Manhattan distance. See details dist.
filter	Whether to filter the input data based on low.cutoff and high.cutoff. Default is FALSE.
low.cutoff	Lower cutoff bound below which will be removed. Default is negative infinity.
high.cutoff	Upper cutoff bound above which will be removed. Default is positive infinity.
return.data	Whether to return the data used to plot. Default is FALSE.
Rowv	Whether to hierarchical cluster the rows. Default is NA. See details heatmap.2.
Colv	Whether to hierarchical cluster the columns Default is NA. See details heatmap.2.
trace	Whether to show the trace line. Defaults is none. See details heatmap.2.
margins	Plot margins. Defaults is c(10,10) See details heatmap.2.
na.color	Color for missing values (NAs). Defaults is black. See details heatmap.2.
key	Whether to show the key. Defaults is TRUE. See details heatmap.2.
show.text	Whether to show title, x-axis and y-axis text. Defaults is TRUE.
...	Additioanl arguments passed to heatmap.2.

Value

Plot a heatmap and optionally return the data used to generate the plot.

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.