spotPlot: Generate Spot Plot

In stevexniu/scMatchmaker: Single Cell Matchmaker

Generate Spot Plot

Description

Generate a spot barplot or dotplot.

Usage

spotPlot(
  interact.strength,
  interact.pval,
  which.cell = NULL,
  which.gene = NULL,
  aggregate = c("none", "row", "column"),
  counted = 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

interact.strength	Interaction strength matrix.
interact.pval	Interaction p-value matrix.
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" (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 barplot. 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.

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