Plot heatmap

Plot a phenotype x phenotype correlation matrix based on genetic overlap.

correlation_heatmap(
  top_targets,
  row_side_vars = c("ancestor_name", "ontLvl"),
  col_side_vars = c("n_celltypes", "n_genes"),
  row_labels = "hpo_name",
  phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(),
  col = pals::gnuplot(),
  show_plot = TRUE,
  save_path = tempfile(fileext = "correlation_heatmap.pdf"),
  height = 10,
  width = height * 1.3,
  fontsize = 7,
  seed = 2023,
  verbose = TRUE
)

Arguments

top_targets

data.table of prioritised targets generated by prioritise_targets.

row_side_vars

Variables to include in row-side metadata annotations.

col_side_vars

Variables to include in column-side metadata annotations.

row_labels

Optional row labels which are put as row names in the heatmap.

phenotype_to_genes

Output of load_phenotype_to_genes mapping phenotypes to gene annotations.

col

A vector of colors if the color mapping is discrete or a color mapping function if the matrix is continuous numbers (should be generated by colorRamp2). If the matrix is continuous, the value can also be a vector of colors so that colors can be interpolated. Pass to ColorMapping. For more details and examples, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#colors .

show_plot

Show the plot.

save_path

Path to save interactive plot to as a self-contained HTML file.

height

Height of the heatmap body.

width

Width of the heatmap body.

fontsize

Axis labels font size.

seed

Set the seed for reproducible clustering.

verbose

Print messages.

Value

Plot

Examples

top_targets <- MSTExplorer::example_targets$top_targets[seq(100),]
hm <- correlation_heatmap(top_targets = top_targets)
#> Constructing HPO gene x phenotype matrix.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> Annotating gene-disease associations with Evidence Score
#> Gathering data from GenCC.
#> Importing cached file.
#> Evidence scores for: 
#>  - 10514 diseases 
#>  - 5171 genes
#> + Version: 2024-12-19
#> Computing all parwise correlations.
#> Aggregating results by group_var='hpo_name'/'hpo_id'/'ancestor_name'/'ontLvl'
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Warning: argument is not numeric or logical: returning NA
#> Creating heatmap: ComplexHeatmap
#> Using palette: okabe
#> Using palette: tol
#> Using palette: okabe
#> Using palette: tol
#> Saving plot --> /tmp/RtmpMmVOaL/file2ffc4c13ebe2correlation_heatmap.pdf