signifPlot: Plots result of signifPlot.

In ellispatrick/spicyR: Spatial analysis of in situ cytometry data

Plots result of signifPlot.

Description

Plots result of signifPlot.

Usage

signifPlot(
  results,
  fdr = FALSE,
  type = "bubble",
  breaks = NULL,
  comparisonGroup = NULL,
  colours = c("#4575B4", "white", "#D73027"),
  marksToPlot = NULL,
  cutoff = 0.05
)

Arguments

results	Data frame obtained from spicy.
fdr	TRUE if FDR correction is used.
type	Where to make a bubble plot or heatmap.
breaks	Vector of 3 numbers giving breaks used in pheatmap. The first number is the minimum, the second is the maximum, the third is the number of breaks.
comparisonGroup	A string specifying the name of the outcome group to compare with the base group.
colours	Vector of colours to use in pheatmap.
marksToPlot	Vector of marks to include in pheatmap.
cutoff	significance threshold for circles in bubble plot

Value

a pheatmap object

Examples

data(spicyTest)
signifPlot(spicyTest, breaks = c(-3, 3, 0.5))

ellispatrick/spicyR documentation built on April 27, 2024, 10:14 a.m.