Skip to contents

plot heatmap without any clustering (use to show NA's)

Source: R/tidyMS_plotting.R
plot_raster.Rd

plot heatmap without any clustering (use to show NA's)

Usage

plot_raster(
  matrix,
  annotation,
  factor_keys,
  sample_name,
  arrange = c("mean", "var"),
  not_na = FALSE,
  show_rownames = FALSE,
  ...
)

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

arrange

either mean or var

not_na

if true than arrange by nr of NA's first and then by arrange

show_rownames

logical, show row names in heatmap

...

additional arguments 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_heatmap_cor(), 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_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$config)
wide <- lfq$data_wide(as.matrix = TRUE)
rs <- plot_raster(wide$data, wide$annotation, lfq$factor_keys(), lfq$sample_name())
stopifnot(class(rs) == "pheatmap")
rs <- plot_raster(wide$data, wide$annotation, lfq$factor_keys(), lfq$sample_name(), "var")
stopifnot(class(rs) == "pheatmap")