plot heatmap with annotations
Usage
plot_heatmap(
matrix,
annotation,
factor_keys,
sample_name,
na_fraction = 0.4,
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
- na_fraction
fraction of NA values per row
- show_rownames
if TRUE shows row names, default FALSE
- ...
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_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_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)
p <- plot_heatmap(wide$data, wide$annotation, lfq$factor_keys(), lfq$sample_name())
stopifnot(class(p) == "pheatmap")