Plot pseudobulk marker heatmap — plot_pseudobulk

Computes mean marker expression per label group and plots a heatmap restricted to relevant markers defined in a lineage table.

Usage

plot_pseudobulk_heatmap(
  spe,
  label_col,
  lineage_table = NULL,
  assay_name = "exprs",
  cell_types = NULL,
  marker_groups = c("pos_markers", "neg_markers"),
  include_all_markers = TRUE,
  drop_unknown = TRUE,
  drop_na = TRUE,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  show_values = TRUE,
  value_digits = 2,
  title = "Pseudobulk marker expression",
  scale = "none",
  row_order = NULL,
  col_order = NULL,
  highlight_lineage = TRUE,
  heatmap_palette = "RdYlBu",
  heatmap_direction = 1,
  text_size = 2.5
)

Arguments

spe: A `SpatialExperiment`/`SingleCellExperiment`.
label_col: Column in `colData(spe)` containing labels.
lineage_table: Tibble with cell_type/pos_markers/neg_markers.
assay_name: Assay name to pull values from. Default "exprs".
cell_types: Optional character vector to restrict label groups.
marker_groups: Which marker sets to include from lineage_table. Default `c("pos_markers", "neg_markers")`.
include_all_markers: Logical; if TRUE, use all assay markers rather than only lineage_table markers. Default TRUE.
drop_unknown: Logical; drop "Unknown" labels. Default TRUE.
drop_na: Logical; drop NA labels. Default TRUE.
cluster_rows: Logical; if TRUE, cluster markers (rows). Default FALSE.
cluster_cols: Logical; if TRUE, cluster labels (cols). Default FALSE.
show_values: Logical; draw mean values on tiles. Default TRUE.
value_digits: Digits for tile labels. Default 2.
title: Plot title. Default "Pseudobulk marker expression".
scale: Scaling for the heatmap. One of "none", "row", or "column". Default "none".
row_order: Optional character vector of marker names to enforce when `cluster_rows = FALSE`. Any missing markers are ignored; any remaining markers not listed are appended in their existing order.
col_order: Optional character vector of label names to enforce when `cluster_cols = FALSE`. Any missing labels are ignored; any remaining labels not listed are appended in their existing order.
highlight_lineage: Logical; draw outlines for lineage markers per cell type. Positive markers are green, negative markers are red. Default FALSE.
heatmap_palette: Palette name for the heatmap. Default "RdYlBu" for a blue-yellow-red diverging scale (pheatmap style). Set to a viridis option (e.g., "viridis", "magma") to use `ggplot2::scale_fill_viridis_c()`.
heatmap_direction: Direction for viridis palettes. Default 1.
text_size: Numeric. Text size for numeric values drawn on heatmap tiles

Value

A `ggplot` object.

Examples

data("cytoGateR_example", package = "cytoGateR")
spe <- cytoGateR_example
labels <- unique(as.character(SummarizedExperiment::colData(spe)$knn_label))
labels <- labels[!is.na(labels)][seq_len(min(2L, sum(!is.na(labels))))]
markers <- rownames(spe)[seq_len(min(3L, nrow(spe)))]
lineage <- data.frame(
  cell_type = labels,
  pos_markers = I(rep(list(markers), length(labels))),
  neg_markers = I(rep(list(character()), length(labels)))
)
plot_pseudobulk_heatmap(
  spe,
  label_col = "knn_label",
  lineage_table = lineage,
  cell_types = labels,
  include_all_markers = FALSE,
  show_values = FALSE
)

#> $plot

#> 
#> $plot_df
#> # A tibble: 6 × 3
#>   marker label expression
#>   <fct>  <fct>      <dbl>
#> 1 MPO    Bcell      0.231
#> 2 MPO    CD8        0.228
#> 3 H3     Bcell      2.44 
#> 4 H3     CD8        2.47 
#> 5 SMA    Bcell      0.253
#> 6 SMA    CD8        0.319
#>