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,
  contextColours = NULL,
  contextLabels = waiver()
)

Arguments

results	A spicy results object
fdr	TRUE if FDR correction is used.
type	Whether to make a bubble plot or heatmap. Note: For survival results a bubble plot will be used.
breaks	Vector of 3 numbers giving breaks used in legend. 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 to colour legend.
marksToPlot	Vector of marks to include in plot.
cutoff	significance threshold for circles in bubble plot.
contextColours	Used for Kontextual results. A named list specifying the colours for each context. By default the Tableau colour palette is used.
contextLabels	Used for Kontextual results. A named list to change the default labels for each context.

Value

a ggplot or pheatmap object

Examples

data(spicyTest)

p <- signifPlot(spicyTest, breaks = c(-3, 3, 0.5))
# plot includes unicode characters, do not use default pdf device
ggplot2::ggsave(p, filename = tempfile(), device = cairo_pdf)

ellispatrick/spicyR documentation built on Dec. 20, 2024, 10:50 a.m.