Create a tidyHeatmap Heatmap for Proteomics

Usage

proteomics_heatmap(
  data,
  mode = c("all", "any", "target"),
  alpha = 0.05,
  comparison = NULL,
  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 = "Proteins",
  column_title = "Samples",
  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 = c("bold", "plain", "italic", "bold.italic"),
  export_path = 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)

mode

Protein filtering mode: "all", "any", or "target"

alpha

Significance threshold for DEP proteins (default: 0.05)

comparison

Name of the comparison for mode "target" (e.g. "B-A")

feature_ids

Vector of specific FeatureIDs to show (default: NULL, uses the mode-based filtering). When supplied, only these proteins are shown and the mode/alpha filtering is ignored.

row_annotation

Row annotations (FeatureIDs). It can be:

Path to a TSV file with a "FeatureID" column plus additional categorical columns
Data frame with the same structure
NULL: no row annotations (default)

row_annotation_cols

Vector of column names to display as annotations. Default: NULL (uses every column except FeatureID)

row_annotation_palette

Named list of palettes, one per annotation. Example: list(Pathway = "brewer:Set1", Function = c("red", "blue", "green"))

row_annotation_size

Width of the row annotation bars. It can be:

Number: interpreted as centimetres (e.g. 0.3 = 0.3cm)
A unit object: grid::unit(0.3, "cm")
NULL: use tidyHeatmap's default value

row_annotation_name_size

Font size of the row annotation names (default: 8)

row_order_by

Row order. It can be:

NULL: no particular ordering (default)
"clustering": order by hierarchical clustering
A column name: order by that annotation (e.g. "Specie")
A vector of columns: order sequentially (e.g. c("Specie", "Process", "Function"))
Include "adjP" when mode = "target" to order by adjusted p-value

split_rows_by

Name of the annotation column used to split the rows into groups (default: NULL)

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: TRUE when <= 50 proteins)

show_column_names

Show the column names (default: TRUE)

palette_value

Palette for the heatmap values (see get_heatmap_palette)

palette_annotation

Palette for the Condition annotation

reverse_palette

Reverse the value palette (default: FALSE)

row_title

Title for the rows

column_title

Title for the columns

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 when mode="target" (default: TRUE)

palette_adjp

Palette for the adjP annotation. It can be:

NULL: use the default palette (red-orange-white)
A vector of 3 colours: c(color_0, color_middle, color_0.05)
String "brewer:name": use an RColorBrewer palette
String "package::palette": use a paletteer palette

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 in degrees (default: 45)

column_dend_height

Height of the column dendrogram. It can be:

Number: interpreted as millimetres (e.g. 30 = 30mm)
A unit object: grid::unit(2, "cm")
NULL: use ComplexHeatmap's default value

row_dend_width

Width of the row dendrogram. Same format as column_dend_height

show_heatmap_legend

Show the heatmap legend (default: TRUE)

show_annotation_legend

Show the annotation legends (default: TRUE)

border_color

Border colour of the heatmap cells. It can be:

NULL or FALSE: no border (default)
TRUE: black border
A colour string: that specific colour (e.g. "black", "grey", "#CCCCCC")

heatmap_title

Main heatmap title (default: NULL, no title)

heatmap_title_size

Font size of the main title (default: 14)

heatmap_title_face

Font face of the title: "plain", "bold", "italic", "bold.italic" (default: "bold")

export_path

Path used to export the heatmap data to TSV (default: NULL, nothing is exported). The file contains FeatureID, the per-sample intensity values, and the metadata (adjP where applicable).

export_file

Path used to export the plot. The format is taken from the extension:

.png: PNG image (raster)
.svg: SVG image (vector)
.pdf: PDF document (vector)

plot_width

Plot width in inches (default: 10). To get pixels: pixels = inches x dpi (e.g. 10" x 300dpi = 3000px)

plot_height

Plot height in inches (default: 8). To get pixels: pixels = inches x dpi (e.g. 8" x 300dpi = 2400px)

export_dpi

Resolution for PNG output in dots per inch (default: 300). Higher dpi = more detail. Common values: 72 (web), 150 (draft), 300 (publication)

Value

tidyHeatmap/ComplexHeatmap object

Examples

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

  # Proteins significant in the B-A comparison, samples grouped by condition
  hm <- proteomics_heatmap(
    res$PCA_Input,
    mode            = "target",
    comparison      = "B-A",
    scale_data      = "row",
    sample_order    = "condition",
    condition_order = c("A", "B", "D")
  )
  print(class(hm))   # print(hm) itself draws it on the current device
}
#> [1] "InputHeatmap"
#> attr(,"package")
#> [1] "tidyHeatmap"