proBatch v1.1.0 ============== Changes: * all functions that deal with data matrix and sample annotation, are checking for sample consistency (discrepancies in sample IDs); * all functions, transforming the data (log, normalization, batch correction) work with both `data_matrix` and `df_long` formats, and called as `[correction_func]_dm` and `[correction_func]_df` correspondingly. * for all `df_long` functions, modifying `measure_col` (Intensity), keeping the old column as: - log_transform_df: beforeLog_[measure_col]; - normalization: preNorm_[measure_col]; - batch correction: preBatchCorr_[measure_col]; - (if adjusting trend): preTrendFit_[measure_col]. Note that this increases the data size. If this is of a concern, use `data_matrix` format instead. * renamed functions: - "center_peptide_batch_medians" to "center_feature_batch_medians" - "normalize_custom_fit" into "adjust_batch_trend"; * harmonised arguments in plotting functions, all of them now take sample annotation and color_list/color_scheme. * simplified color scheme definition and usage, which is now consistent over all plotting functions (check updated argument definitions!) * Added internal automated definition of color scheme (useful when single plotting functions are used, and color scheme consistency is not critical); * consistent handling of missing values by proteome-wide diagnostic functions; * renamed "plot_heatmap" into "plot_heatmap_diagnostic" as now "plot_heatmap_generic" is added for non-standard cases of heatmap plotting; * better legend for DateTime color mapping in meanplots, boxplots and feature-level plots.