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Gene-immune correlation butterfly plot

Source: R/GeneImmuneCorPlot.R
GeneImmuneCorPlot.Rd

Draw a linkET-style correlation butterfly plot. The heatmap shows immune-cell or immune-signature correlations, and curved links show correlations between target genes and immune abundances.

Usage

GeneImmuneCorPlot(
  object = NULL,
  gene.data = NULL,
  immune.data = NULL,
  features,
  immune.cols = NULL,
  assay = NULL,
  layer = "data",
  cor_method = c("spearman", "pearson", "kendall"),
  p_cutoff = 0.05,
  abs_cor_breaks = c(0.2, 0.4),
  heatmap_colors = c("#2166AC", "#67A9CF", "#F7F7F7", "#F4A582", "#B2182B"),
  link_colors = c(Positive = "#E71D36", Negative = "#0073C2", Not = "grey82"),
  link_sizes = c(`>= 0.4` = 1.5, `0.2 - 0.4` = 0.8, `< 0.2` = 0.3),
  title = NULL,
  subtitle = NULL,
  theme_use = "theme_scop",
  theme_args = list(),
  verbose = TRUE
)

Arguments

object

Optional Seurat, SummarizedExperiment, deconvolution bundle, or matrix-like object used to resolve expression and immune abundance data.

gene.data

Optional gene expression matrix with genes in rows and samples in columns.

immune.data

Optional immune abundance matrix with samples in rows and immune cell types or signatures in columns.

features

Target genes to correlate with immune abundance.

immune.cols

Metadata columns to extract from a Seurat object.

assay

Assay used for Seurat or SummarizedExperiment expression.

layer

Assay layer used for Seurat expression.

cor_method

Correlation method. Default is "spearman".

p_cutoff

P-value cutoff used for positive/negative link categories.

abs_cor_breaks

Two numeric breakpoints for link width categories. Default c(0.2, 0.4) creates < 0.2, 0.2 - 0.4, and >= 0.4.

heatmap_colors

Continuous colors for immune-cell correlations.

Colors for Positive, Negative, and Not links.

Link sizes for strong, medium, and weak absolute correlations.

title, subtitle

Plot title and subtitle.

theme_use

Theme function name.

theme_args

Additional theme arguments.

verbose

Whether to print progress messages.

Value

A ggplot object.