Build a List of Heatmaps for Several Subsets — proteomics_heatmap

Automatically builds heatmaps for "all", "any" and/or specific comparisons.

Usage

proteomics_heatmap_list(
  data,
  modes = c("all", "any"),
  alpha = 0.05,
  feature_ids = NULL,
  row_annotation = NULL,
  row_annotation_cols = NULL,
  row_annotation_palette = NULL,
  row_annotation_size = NULL,
  row_annotation_name_size = 8,
  row_order_by = NULL,
  split_rows_by = NULL,
  scale_data = c("row", "none", "column"),
  sample_order = "clustering",
  condition_order = NULL,
  cluster_rows = FALSE,
  cluster_columns = TRUE,
  show_row_names = NULL,
  show_column_names = TRUE,
  palette_value = NULL,
  palette_annotation = NULL,
  reverse_palette = FALSE,
  row_title_size = 10,
  column_title_size = 10,
  show_row_title = TRUE,
  show_column_title = TRUE,
  show_annotation = TRUE,
  split_by_condition = FALSE,
  show_adjp_annotation = TRUE,
  palette_adjp = NULL,
  row_names_size = 7,
  column_names_size = 9,
  column_names_rotation = 45,
  column_dend_height = NULL,
  row_dend_width = NULL,
  show_heatmap_legend = TRUE,
  show_annotation_legend = TRUE,
  border_color = NULL,
  heatmap_title = NULL,
  heatmap_title_size = 14,
  heatmap_title_face = "bold",
  export_path = NULL,
  export_modes = NULL,
  export_file = NULL,
  plot_width = 10,
  plot_height = 8,
  export_dpi = 300
)

Arguments

data: Data frame in long format (see prepare_heatmap_data for the structure)
modes: Vector of modes to generate: "all", "any", and/or comparison names (default: c("all", "any"))
alpha: Significance threshold for DEP proteins (default: 0.05)
feature_ids: Vector of specific FeatureIDs to show (default: NULL)
row_annotation: Row annotations (TSV path or data.frame)
row_annotation_cols: Columns to use as row annotations
row_annotation_palette: List of palettes for the row annotations
row_annotation_size: Width of the row annotation bars (a number in cm, or a unit)
row_annotation_name_size: Font size of the row annotation names (default: 8)
row_order_by: Row order: "clustering", annotation column(s), or include "adjP" for mode="target"
split_rows_by: Annotation column used to split the rows into groups
scale_data: Scaling type: "none", "row", "column" (default: "row")
sample_order: Sample order: "clustering", "condition", or a custom vector
condition_order: Condition order when sample_order = "condition"
cluster_rows: Cluster the rows (default: FALSE)
cluster_columns: Cluster the columns (default: TRUE)
show_row_names: Show the row names (default: auto)
show_column_names: Show the column names (default: TRUE)
palette_value: Palette for the heatmap values
palette_annotation: Palette for the Condition annotation
reverse_palette: Reverse the value palette (default: FALSE)
row_title_size: Font size of the row title (default: 10)
column_title_size: Font size of the column title (default: 10)
show_row_title: Show the row title (default: TRUE)
show_column_title: Show the column title (default: TRUE)
show_annotation: Show the Condition annotation (default: TRUE)
split_by_condition: Split the heatmap by condition (default: FALSE)
show_adjp_annotation: Show the adjP row annotation for comparisons (default: TRUE)
palette_adjp: Palette for the adjP annotation (see proteomics_heatmap)
row_names_size: Font size of the row names (default: 7)
column_names_size: Font size of the column names (default: 9)
column_names_rotation: Rotation of the column names (default: 45)
column_dend_height: Height of the column dendrogram (a number in mm, or a unit)
row_dend_width: Width of the row dendrogram (a number in mm, or a unit)
show_heatmap_legend: Show the heatmap legend (default: TRUE)
show_annotation_legend: Show the annotation legends (default: TRUE)
border_color: Border colour of the cells (NULL, TRUE, or a colour)
heatmap_title: Main heatmap title (default: NULL, no title). "{mode}" can be used as a placeholder, and is replaced by the mode name
heatmap_title_size: Font size of the main title (default: 14)
heatmap_title_face: Font face of the title (default: "bold")
export_path: Base path used to export the data to TSV (default: NULL). The mode name is appended to the file name (e.g. "export_all.tsv", "export_B-A.tsv")
export_modes: Vector of modes to export (default: NULL, exports all of them). Only relevant when export_path is set. Example: c("all", "B-A")
export_file: Base path used to export the plots. The mode is appended to the name. The format is taken from the extension (.png, .svg, .pdf)
plot_width: Plot width in inches (default: 10)
plot_height: Plot height in inches (default: 8)
export_dpi: Resolution for PNG output in dots per inch (default: 300)

Value

Named list of tidyHeatmap objects

Examples

if (requireNamespace("ComplexHeatmap", quietly = TRUE) &&
    requireNamespace("tidyHeatmap", quietly = TRUE)) {
  data(nadia_dia)
  res <- process_proteomics(nadia_dia, verbose = FALSE)

  # "any" plus one heatmap per named comparison
  hm_list <- proteomics_heatmap_list(
    res$PCA_Input,
    modes           = c("any", "B-A"),
    sample_order    = "condition",
    condition_order = c("A", "B", "D"),
    palette_value   = "brewer:RdYlBu"
  )
  print(names(hm_list))   # print(hm_list[["B-A"]]) draws one of them
}
#> [1] "any" "B-A"