PlotSpot: Interaction Spot Plot

In stevexniu/scMatchmaker: Single Cell Matchmaker

Interaction Spot Plot

Description

Generate a spot plot for cell-cell interactions similar to the bertin plot. The size or height of the dot or bar represents the interaction strength. The color of the bars and dots represents the p values.

Usage

PlotSpot(
  object,
  which.cell = NULL,
  which.gene = NULL,
  aggregate = c("none", "cell", "gene"),
  counted = FALSE,
  selected = FALSE,
  color = "RdBu",
  color.bins = 7,
  type = c("dot", "bar"),
  order = FALSE,
  order.dist = "minkowski",
  p = 1,
  filter = FALSE,
  low.cutoff = -Inf,
  high.cutoff = Inf,
  dot.scale = 8,
  plot.y.axis = TRUE,
  fix.y.axis = TRUE,
  do.return = FALSE
)

Arguments

object	Matchmaker object.
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. cell, aggregated by cell-cell interactions strengths (Default). gene, aggregated by ligand-receptor pairs strengths. none, no aggregation.
counted	Aggregate interactions counts instead of strengths. Default is FALSE.
selected	Use selected data if calculated. Default is FALSE.
color	Color palette name. Default is "RdBu" (reversed order), high values are in blue and low values in red See details brewer.pal.
color.bins	Number of differen colors in pallete. Default is 7. See detail brewer.pal.
type	Types of plot. Default is dotplot. dot, dotplot or bertin plot (Default). bar, barplot.
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.
dot.scale	Scale the size of the dots. Default is 8.
plot.y.axis	Whether to show y axis for each barplot. Default is TRUE.
fix.y.axis	Whether to fix the all barplot ticks or use the relative ticks for each barplot. Default is TRUE.
do.return	Whether to return the data used to plot. Default is FALSE.

Value

A ggplot object or a list with strength and p value data used to generate the plot.

Examples

## Not run: 
 PlotSpot(object, which.cell = 1:10, which.gene = 1:10)

## End(Not run)

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