Immune abundance plots — ImmuneAbundancePlot • scop

Visualize immune abundance or score matrices from deconvolution results, spatial metadata, GSVA-like scores, or user-provided matrices.

Usage

ImmuneAbundancePlot(
  object = NULL,
  immune.data = NULL,
  immune.cols = NULL,
  group.by = NULL,
  group.data = NULL,
  plot_type = c("heatmap", "bar", "box", "cor"),
  sample_order = NULL,
  cell_type_order = NULL,
  scale = c("none", "row", "column"),
  cor_method = c("spearman", "pearson", "kendall"),
  bar_position = c("stack", "fill"),
  show_sample_names = FALSE,
  show_cor_label = FALSE,
  cor_label_size = 3,
  add_stat = FALSE,
  comparisons = NULL,
  pairwise_method = "wilcox.test",
  sig_label = c("p.signif", "p.format"),
  sig_labelsize = 3.5,
  box_width = 0.64,
  box_alpha = 0.92,
  pt.size = 1.35,
  pt.alpha = 0.72,
  jitter.width = 0.12,
  grid_major = FALSE,
  palette = "Chinese",
  palcolor = NULL,
  heatmap_palette = "YlGnBu",
  heatmap_palcolor = NULL,
  title = NULL,
  subtitle = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list()
)

Arguments

object: Optional SummarizedExperiment, Seurat, deconvolution bundle, or matrix-like object.
immune.data: Optional abundance matrix with samples/spots/cells in rows and immune cell types or signatures in columns.
immune.cols: Metadata columns to extract from a Seurat object. If NULL, columns matching RCTD_prop_*, *_prop_*, or *_frac_* are used.
group.by: Optional grouping column for bar and box plots.
group.data: Optional named vector or data frame containing sample groups when groups cannot be inferred from object.
plot_type: Plot type: "heatmap", "bar", "box", or "cor".
sample_order: Optional sample order.
cell_type_order: Optional immune cell type or signature order.
scale: Scaling for heatmap values: "none", "row", or "column".
cor_method: Correlation method for plot_type = "cor".
bar_position: Bar position for plot_type = "bar". "stack" shows raw abundance; "fill" rescales each sample to 1.
show_sample_names: Whether to show sample names in heatmap and bar plots.
show_cor_label: Whether to print correlation values in cor plots.
cor_label_size: Text size for correlation labels.
add_stat: Whether to add group comparison labels to box plots. Requires ggpubr.
comparisons: Optional group comparisons passed to ggpubr::stat_compare_means().
pairwise_method: Statistical test for box plot comparisons.
sig_label: Significance label type for ggpubr::stat_compare_means().
sig_labelsize: Significance label size.
box_width, box_alpha: Box plot width and alpha.
pt.size, pt.alpha, jitter.width: Point size, alpha, and jitter width.
grid_major: Whether to show major y grid lines for bar and box plots.
palette: Discrete palette for grouped plots.
palcolor: Optional custom discrete colors.
heatmap_palette: Continuous palette name for heatmaps.
heatmap_palcolor: Optional custom continuous colors.
title, subtitle: Plot title and subtitle.
legend.position: Legend position.
legend.direction: Legend direction.
theme_use: Theme function name.
theme_args: Additional theme arguments.

Value

A ggplot object.