Jaccard Similarity Heatmap

Computes pairwise Jaccard similarity between groups based on a set of named variables (e.g. top genes, features), then draws a colour-coded heatmap with optional numeric labels per cell and optional coloured axis strips.

Usage

PlotHeatmapJaccard(
  data,
  group_col = "cell_type",
  name_col = "gene",
  title = "Jaccard Similarity",
  group_levels = NULL,
  midpoint = 0.1,
  text_size = 2.5,
  show_diag = FALSE,
  low_color = "white",
  high_color = "#B2182B",
  show_strip = FALSE,
  strip_colors = NULL,
  strip_size = 0.45,
  return_type = c("plot", "data", "both"),
  filename = NULL,
  width = 10,
  height = 9,
  dpi = 300
)

Arguments

data

A data.frame containing at least a group column and a name column.

group_col

Column name for the grouping variable (e.g. cell type). Default "cell_type".

name_col

Column name for the feature/gene names used to compute Jaccard similarity. Default "gene".

title

Plot title. Default "Jaccard Similarity".

group_levels

Character vector specifying the display order of groups on both axes. NULL = factor levels (if factor) or data appearance order.

midpoint

Midpoint of the colour gradient. Default 0.1.

text_size

Size of the numeric labels inside each cell. Default 2.5. Set to 0 to hide labels.

show_diag

Logical. Whether to show diagonal values. Default FALSE (diagonal is set to NA and shown in grey).

low_color

Low end of the fill gradient. Default "white".

high_color

High end of the fill gradient. Default "#B2182B".

show_strip

Logical. Whether to draw coloured annotation strips along the top (X axis) and left (Y axis) of the heatmap. Default FALSE.

strip_colors

Character vector of colours for each group strip. NULL = auto palette (same order as group_levels / ct_names).

strip_size

Numeric. Width/height of the colour strip in data units. Default 0.45.

return_type

What to return: "plot" (default, the ggplot object), "data" (the Jaccard similarity matrix), or "both" (a list with elements plot and matrix).

filename

Output file path. NULL = no save.

width

Output width in inches. Default 10.

height

Output height in inches. Default 9.

dpi

Output resolution. Default 300.

Value

Depends on return_type:

"plot"

A ggplot object (default).

"data"

A numeric matrix of pairwise Jaccard similarities.

"both"

A list with elements plot and matrix.

Examples

if (FALSE) { # \dontrun{
library(ToyData)
data(Toy_gene_importance)

# Basic Jaccard heatmap
PlotHeatmapJaccard(Toy_gene_importance, name_col = "gene")

# With coloured axis strips
PlotHeatmapJaccard(Toy_gene_importance, name_col = "gene", show_strip = TRUE)

# Custom title and return matrix
res <- PlotHeatmapJaccard(Toy_gene_importance, name_col = "gene",
                           title = "Gene Importance Jaccard",
                           return_type = "both")
res$matrix
} # }