Plot feature data and result of aggregation
plot_estimate(data, config, data_aggr, config_reduced, show.legend = FALSE)Other plotting:
ContrastsPlotter,
INTERNAL_FUNCTIONS_BY_FAMILY,
UpSet_interaction_missing_stats(),
UpSet_missing_stats(),
medpolish_estimate_df(),
missigness_histogram(),
missingness_per_condition(),
missingness_per_condition_cumsum(),
plot_NA_heatmap(),
plot_heatmap(),
plot_heatmap_cor(),
plot_heatmap_cor_iheatmap(),
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(),
plot_screeplot()
Other aggregation:
INTERNAL_FUNCTIONS_BY_FAMILY,
aggregate_intensity_topN(),
estimate_intensity(),
intensity_summary_by_hkeys(),
medpolish_estimate(),
medpolish_estimate_df(),
medpolish_estimate_dfconfig(),
medpolish_protein_estimates(),
plot_hierarchies_add_quantline(),
plot_hierarchies_line(),
plot_hierarchies_line_df(),
rlm_estimate(),
rlm_estimate_dfconfig()
istar <- sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
config <- istar$config
analysis <- istar$data
analysis <- prolfqua::transform_work_intensity(analysis, config, log2)
#> Column added : log2_abundance
bbMed <- estimate_intensity(analysis, config, .func = medpolish_estimate_dfconfig)
#> starting aggregation
tmpMed <- plot_estimate(analysis, config, bbMed$data, bbMed$config)
stopifnot("ggplot" %in% class(tmpMed$plots[[1]]))
stopifnot("ggplot" %in% class(tmpMed$plots[[2]]))
bbRob <- estimate_intensity(analysis, config, .func = rlm_estimate_dfconfig)
#> starting aggregation
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
tmpRob <- plot_estimate(analysis, config, bbRob$data, bbRob$config)
stopifnot("ggplot" %in% class(tmpRob$plots[[1]]))
stopifnot("ggplot" %in% class(tmpRob$plots[[2]]))