PlotHeatmap: Interaction Heatmap

In stevexniu/scMatchmaker: Single Cell Matchmaker

Interaction Heatmap

Description

Plot a interaction heatmap.

Usage

PlotHeatmap(
  object,
  data = c("strength", "pvalue", "data"),
  which.cell = NULL,
  which.gene = NULL,
  aggregate = c("none", "cell", "gene"),
  counted = FALSE,
  selected = FALSE,
  scale = c("none", "cell", "gene"),
  scale_max = Inf,
  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

object	Matchmaker object.
data	Data to plot. Default is interaction strength. strength, Interaction strength. pvalue, Interaction p value. data, expression data.
which.cell	Interacting cell type name (saperated by '|' i.e 'DC|Mac') or index to plot. Default is NULL.
which.gene	Interacting gene name (saperated by '_' i.e 'CSF1_CSF1R') or index to plot. Default is NULL.
aggregate	Type of aggregation used. Default is none. none, no aggregation. cell, aggregated by cell-cell interactions. gene, aggregated by ligand-receptor pairs.
counted	Aggregate interactions counts instead of strengths. Default is FALSE.
selected	Use selected data if calculated. Default is FALSE.
scale	Scale and center data. Default is none. none, no scaling. cell, scale data by cell (row). gene, scale data by gene (column).
scale_max	Maximum cutoff for scaled data. Default is Inf.
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.

Examples

## Not run: 
 PlotHeatmap(object, data = "strength", aggregate = "row")

## End(Not run)

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