Colocalization Heatmap Visualization

Generates a heatmap to visualize the colocalization indices between SE cell states, optionally annotating significance levels based on p-values. The heatmap includes customizable row and column annotations, color scales, clustering, and significance indicators.

Usage

ColocalizationHeatmapView(
  ColocIndex,
  Pval = NULL,
  breaks = quantile(ColocIndex, c(0.55, 0.75, 0.9)),
  colors = c("#f2f0f7", "#cbc9e2", "#54278f"),
  legend_height = 1,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  show_left_legend = FALSE,
  show_column_names = FALSE,
  show_row_names = FALSE,
  ...
)

Arguments

ColocIndex

A numeric matrix of colocalization indices. Row names should be formatted as "SE_CellType".

Pval

Optional named numeric vector of p-values for each SE. Names should match SE identifiers.

breaks

Numeric vector specifying break points for the heatmap color scale. Default is the 55th, 75th, and 90th quantiles of ColocIndex.

colors

Character vector of colors for the heatmap. Default is c("#f2f0f7", "#cbc9e2", "#54278f").

legend_height

Numeric, height of the legend. Default is 1.

cluster_rows

Logical, whether to cluster rows. Default is FALSE.

cluster_cols

Logical, whether to cluster columns. Default is FALSE.

show_left_legend

Logical, whether to show the left-side legend. Default is FALSE.

show_column_names

Logical, whether to show column names. Default is FALSE.

show_row_names

Logical, whether to show row names. Default is FALSE.

...

Additional arguments passed to HeatmapView.

Value

A ComplexHeatmap object visualizing colocalization between cell states.

Details

This function splits the row names into two parts: SE (spatial ecosystem) and CellType, and assigns colors to both categories. If Pval is provided, significance levels are annotated using "*", "**", "***", or "****" for p-values <0.05, <0.01, <0.001, and <0.0001, respectively. The heatmap can be customized with clustering, annotations, and color scales.

Examples

# Example usage
col_matrix <- matrix(runif(25), nrow = 5)
rownames(col_matrix) <- c("SE1_CD4T", "SE1_CD8T", "SE2_CD4T", "SE2_CD8T", "SE3_CD4T")
colnames(col_matrix) <- c("SE1_CD4T", "SE1_CD8T", "SE2_CD4T", "SE2_CD8T", "SE3_CD4T")
pvals <- c(SE1 = 0.01, SE2 = 0.2, SE3 = 0.0005)
ColocalizationHeatmapView(col_matrix, Pval = pvals)
#> Loading required package: pals
#> Warning: `legend_height` you specified is too small, use the default minimal
#> height.
#> Warning: `legend_height` you specified is too small, use the default minimal
#> height.
#> Warning: `legend_height` you specified is too small, use the default minimal
#> height.