Skip to contents

plot correlation heatmap with annotations

Source: R/tidyMS_plotting.R
plot_heatmap_cor.Rd

plot correlation heatmap with annotations

Usage

plot_heatmap_cor(
  matrix,
  annotation,
  factor_keys,
  sample_name,
  R2 = FALSE,
  color = colorRampPalette(c("white", "red"))(1024),
  ...
)

Arguments

matrix

numeric matrix — wide-format intensity data

annotation

data.frame — sample annotation

factor_keys

character vector — factor column names for annotation

sample_name

character — sample name column

R2

logical — plot R-squared instead of correlation

color

color palette

...

passed to pheatmap

See also

Other plotting: ContrastsPlotter, INTERNAL_FUNCTIONS_BY_FAMILY, medpolish_estimate_df(), missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), plot_estimate(), plot_heatmap(), plot_hierarchies_add_quantline(), plot_hierarchies_boxplot_df(), plot_hierarchies_line(), plot_hierarchies_line_df(), plot_intensity_distribution_violin(), plot_na_heatmap(), plot_pca(), plot_raster(), plot_sample_correlation(), upset_interaction_missing_stats(), upset_missing_stats()

Examples


istar <- sim_lfq_data_protein_config()
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
lfq <- LFQData$new(istar$data, istar$config)
wide <- lfq$to_wide(as.matrix = TRUE)
pheat_map <- plot_heatmap_cor(wide$data, wide$annotation,
  lfq$factor_keys(), lfq$sample_name())
stopifnot("pheatmap" %in% class(pheat_map))
pheat_map <- plot_heatmap_cor(wide$data, wide$annotation,
  lfq$factor_keys(), lfq$sample_name(), R2 = TRUE)
stopifnot("pheatmap" %in% class(pheat_map))