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plot heatmap of NA values

Source: R/tidyMS_plotting.R
plot_NA_heatmap.Rd

plot heatmap of NA values

Usage

plot_na_heatmap(
  matrix,
  annotation,
  factor_keys,
  sample_name,
  limitrows = 10000,
  distance = "binary"
)

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

limitrows

max rows to display

distance

distance method for clustering

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_pca(), plot_raster(), plot_sample_correlation(), upset_interaction_missing_stats(), upset_missing_stats()

Examples


istar <- sim_lfq_data_peptide_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)
tmp <- plot_na_heatmap(wide$data, wide$annotation, lfq$factor_keys(), lfq$sample_name())
#> rows with NA's: 16; all rows :28
stopifnot(class(tmp) == "pheatmap")