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Plot IREA response or polarization results

Source: R/IREAPlot.R
IREAPlot.Rd

Display enrichment effects and reference-cell significance.

Usage

IREAPlot(
  object,
  plot_type = c("compass", "radar", "dotplot", "heatmap"),
  padjustCutoff = 0.05,
  palette = "Chinese",
  palcolor = NULL,
  theme_use = "theme_scop"
)

Arguments

object

An irea_result, a Seurat object containing object@tools$IREA, or a named list of results for dotplots and heatmaps.

plot_type

One of "compass", "radar", "dotplot", or "heatmap".

padjustCutoff

Significance threshold used for compass colouring and the radar display. Radar scores are zero when no positive effect meets this threshold; otherwise all positive effects are divided by their maximum.

palette, palcolor

Palette name and optional custom colours passed to thisplot::palette_colors(). For compass plots, colours map to Positive, Negative and Not significant, in that order.

theme_use

Theme name, function or ggplot theme, as in other package plots.

Value

An editable ggplot object; plotting does not change result statistics.

References

Cui, Ang; Huang, Teddy; Li, Shuqiang; Ma, Aileen; Perez, Jorge L.; Sander, Chris; Keskin, Derin B.; Wu, Catherine J.; Fraenkel, Ernest; Hacohen, Nir. Dictionary of immune responses to cytokines at single-cell resolution. Nature 625, 377-384 (2024). doi:10.1038/s41586-023-06816-9.

Examples

if (FALSE) { # \dontrun{
reference <- PrepareDB(
  db = "IREA_Macrophage", species = "Homo_sapiens"
)[["Homo_sapiens"]][["IREA_Macrophage"]]
result <- RunIREA(c("ISG15", "IFIT3", "BST2"), reference = reference)
IREAPlot(result, palette = "Chinese")
} # }