Ben's New Features [testing: TODO]

.gitattributes

@@ -0,0 +1 @@
+man/*.Rd linguist-generated=true

DESCRIPTION

@@ -13,81 +13,87 @@ Description: A collection of customized functions used for
     convenient nested linear models, machine learning utilities, etc.
 License: Artistic-2.0
 biocViews: Proteomics, MassSpectrometry
-Depends:
+Depends: 
     R (>= 3.5.0),
     MSnbase
-Imports:
+Imports: 
     Biobase,
-    BiocGenerics,
     BiocParallel,
     Biostrings,
     Boruta,
     car,
-    ComplexHeatmap,
     circlize,
+    clusterProfiler,
+    ComplexHeatmap,
+    cowplot,
     data.table, 
     doParallel,
     DOSE,
     dplyr,
-    foreach,
+    enrichplot,
+    FField,
     forcats,
+    foreach,
+    fuzzyjoin,
+    ggh4x,
     ggplot2,
+    ggridges,
     ggrepel, 
     glmnet,
     glue,
     gplots,
+    graphics,
+    grDevices,
     grid,
     Heatplus,
     invgamma,
     iterators,
+    knitr,
     limma,
     lme4,
-    Matrix, 
     methods,
+    msmsTests,
+    MSnID,
+    org.Hs.eg.db,
     outliers,
+    pals,
     parallel,
+    pROC, 
     purrr, 
     qvalue, 
     randomForest,
     reshape2, 
     rlang,
     ROCR,
-    pROC,
     scales,
-    stats,
+    shapviz,
     statmod,
+    stats,
     stringr,
     sva,
-    tibble, 
-    tidyr, 
+    tibble,
+    tidyr,
     tidyselect,
-    umap, 
+    tools,
+    treeshap,
+    umap,
     utils,
     varSelRF,
+    viridis,
     WGCNA,
-    xtable,
-    FField,
-    MSnID
-Suggests:
+    xtable
+Suggests: 
     BiocStyle,
     biomaRt,
-    clusterProfiler,
     e1071,
-    enrichplot,
     ggforce,
-    ggnewscale,
     GOstats,
-    knitr,
-    msmsTests,
-    org.Hs.eg.db,
-    qpdf,
-    RColorBrewer, 
+    RColorBrewer,
     ReactomePA,
     rmarkdown,
-    UniProt.ws,
-    viridis
+    UniProt.ws
 Remotes: 
     github::cran/FField,
     github::PNNL-Comp-Mass-Spec/MSnID@pnnl-master
 VignetteBuilder: knitr
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,20 +1,36 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.do_batch_correction)
+export(.do_filter)
+export(.do_normalize)
+export(.raw)
 export(ComBat.NA)
 export(PeCorA)
 export(adjust_for_parent_protein_profiles)
 export(blue.colors)
 export(complex_heatmap)
 export(concatenate_by_features)
+export(copy_raw_files_from_dms)
 export(correct_batch_effect)
 export(correct_batch_effect_NA)
 export(correct_batch_effect_empiricalBayesLM)
+export(create_boxplot)
+export(create_faceted_density_plot)
+export(create_feature_count)
+export(create_layered_density_plot)
+export(create_missingness)
+export(create_msnset)
+export(create_multi_pca)
+export(create_overall_correlation_heatmap)
+export(create_samples_correlation_heatmap)
 export(dist)
 export(dusk.colors)
 export(eset_lm)
 export(eset_presence_absence)
 export(evaluate_parameter_effect)
 export(exhaustive_ratios)
+export(export_data_levels)
+export(export_exprs)
 export(filter_by_occurrence)
 export(heatmap.3)
 export(heatmap.plus.2)
@@ -39,6 +55,7 @@ export(normalizeByGlob)
 export(normalizeByRef)
 export(normalize_by_feature_property)
 export(normalize_by_feature_property_partitioned)
+export(organize_mzml_by_plex)
 export(paircomp)
 export(peptide_significance_map)
 export(plotAUC)
@@ -48,11 +65,13 @@ export(plot_annHeatmap2)
 export(plot_feature)
 export(plot_pca)
 export(plot_sel_feat_with_p_vals)
+export(plot_treeshap)
 export(plot_umap)
 export(plot_upset)
 export(plot_volcano)
 export(protein_inference)
 export(ptm_significance_map)
+export(qc_report)
 export(readMaxQuantPeptideCounts)
 export(readMaxQuantPeptides)
 export(readMaxQuantProtGroups)
@@ -65,11 +84,14 @@ export(remove_covariate)
 export(rf_modeling)
 export(rollup_using_representative)
 export(rrollup)
+export(run_msConvert_cli)
 export(subset_by_size)
 export(turbo.colors)
+export(write_plex_annotation_files)
 export(xtable2)
 exportMethods(map_peptide_position)
 import(ComplexHeatmap)
+import(dplyr)
 import(ggplot2)
 import(glmnet)
 import(grid)
@@ -89,6 +111,11 @@ importFrom(BiocParallel,bpparam)
 importFrom(Biostrings,readAAStringSet)
 importFrom(Boruta,Boruta)
 importFrom(Boruta,getSelectedAttributes)
+importFrom(ComplexHeatmap,Heatmap)
+importFrom(ComplexHeatmap,HeatmapAnnotation)
+importFrom(ComplexHeatmap,draw)
+importFrom(ComplexHeatmap,max_text_width)
+importFrom(ComplexHeatmap,rowAnnotation)
 importFrom(DOSE,geneInCategory)
 importFrom(FField,FFieldPtRep)
 importFrom(Heatplus,RainbowPastel)
@@ -103,12 +130,14 @@ importFrom(MSnbase,exprs)
 importFrom(MSnbase,fData)
 importFrom(MSnbase,featureNames)
 importFrom(MSnbase,pData)
+importFrom(MSnbase,plotNA)
 importFrom(MSnbase,sampleNames)
 importFrom(ROCR,performance)
 importFrom(ROCR,prediction)
 importFrom(WGCNA,empiricalBayesLM)
 importFrom(car,Anova)
 importFrom(circlize,colorRamp2)
+importFrom(cowplot,plot_grid)
 importFrom(data.table,fread)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
@@ -149,18 +178,27 @@ importFrom(dplyr,sym)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(dplyr,where)
+importFrom(forcats,fct_rev)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
+importFrom(ggh4x,facet_nested)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
+importFrom(ggplot2,after_stat)
+importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expansion)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_abline)
+importFrom(ggplot2,geom_boxplot)
+importFrom(ggplot2,geom_col)
+importFrom(ggplot2,geom_density)
 importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_jitter)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_linerange)
 importFrom(ggplot2,geom_point)
@@ -169,14 +207,18 @@ importFrom(ggplot2,geom_rect)
 importFrom(ggplot2,geom_ribbon)
 importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,geom_text)
+importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,position_stack)
+importFrom(ggplot2,rel)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_fill_gradient)
 importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,scale_fill_gradientn)
 importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,sec_axis)
@@ -186,12 +228,16 @@ importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,theme_minimal)
+importFrom(ggplot2,unit)
 importFrom(ggplot2,vars)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,xlim)
 importFrom(ggplot2,ylab)
 importFrom(ggplot2,ylim)
 importFrom(ggrepel,geom_label_repel)
+importFrom(ggridges,geom_density_ridges)
+importFrom(ggridges,theme_ridges)
+importFrom(glue,glue)
 importFrom(gplots,bluered)
 importFrom(gplots,heatmap.2)
 importFrom(grDevices,bmp)
@@ -218,9 +264,13 @@ importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(graphics,rect)
 importFrom(graphics,title)
+importFrom(grid,gpar)
+importFrom(grid,grid.rect)
+importFrom(grid,grid.text)
 importFrom(grid,unit)
 importFrom(invgamma,dinvgamma)
 importFrom(iterators,icount)
+importFrom(knitr,include_graphics)
 importFrom(limma,eBayes)
 importFrom(limma,lmFit)
 importFrom(limma,topTable)
@@ -230,6 +280,7 @@ importFrom(outliers,grubbs.test)
 importFrom(outliers,outlier)
 importFrom(pROC,ci.se)
 importFrom(pROC,roc)
+importFrom(pals,glasbey)
 importFrom(parallel,clusterApply)
 importFrom(parallel,clusterEvalQ)
 importFrom(parallel,clusterExport)
@@ -254,12 +305,16 @@ importFrom(rlang,parse_expr)
 importFrom(rlang,sym)
 importFrom(scales,alpha)
 importFrom(scales,hue_pal)
+importFrom(scales,label_number)
 importFrom(scales,log_breaks)
 importFrom(scales,pretty_breaks)
 importFrom(scales,rescale)
 importFrom(scales,scientific_format)
+importFrom(scales,squish)
 importFrom(scales,trans_new)
 importFrom(scales,viridis_pal)
+importFrom(shapviz,get_shap_values)
+importFrom(shapviz,shapviz)
 importFrom(stats,aggregate)
 importFrom(stats,anova)
 importFrom(stats,as.dendrogram)
@@ -309,6 +364,7 @@ importFrom(stringr,str_detect)
 importFrom(stringr,str_length)
 importFrom(stringr,str_locate_all)
 importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split_i)
 importFrom(stringr,str_sub)
 importFrom(sva,ComBat)
 importFrom(tibble,column_to_rownames)
@@ -318,11 +374,15 @@ importFrom(tidyr,fill)
 importFrom(tidyr,gather)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
 importFrom(tidyr,separate_rows)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
 importFrom(tidyselect,any_of)
 importFrom(tidyselect,contains)
+importFrom(tools,toTitleCase)
+importFrom(treeshap,treeshap)
+importFrom(treeshap,unify)
 importFrom(umap,umap)
 importFrom(umap,umap.defaults)
 importFrom(utils,flush.console)
@@ -334,6 +394,9 @@ importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
 importFrom(varSelRF,varSelRF)
+importFrom(viridis,scale_color_viridis)
+importFrom(viridis,scale_fill_viridis)
+importFrom(viridis,viridis)
 importFrom(xtable,print.xtable)
 importFrom(xtable,xtable)
 importMethodsFrom(MSnID,map_peptide_position)

R/PeCorA.R

@@ -1,12 +1,4 @@
 #' @title Peptide Correlation Analysis (PeCorA)
-#'
-#' @description Perform Peptide Correlation Analysis (PeCorA) as described in
-#'   \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592057/}.
-#'
-#' @param m \code{MSnSet} object with pData and fData tables. fData must have
-#'   columns \code{protein_column} and \code{peptide_column}. The exprs data
-#'   should be aggregated such that features are unique combinations of peptide
-#'   and protein.
 #' @param proteins character; one or more proteins in
 #'   \code{fData(m)[[protein_column]]} with peptides to test. Only those
 #'   proteins with at least 2 peptides will be considered.
@@ -54,7 +46,7 @@
 #' @references Dermit, M., Peters-Clarke, T. M., Shishkova, E., & Meyer, J. G.
 #'   (2021). Peptide Correlation Analysis (PeCorA) Reveals Differential
 #'   Proteoform Regulation. \emph{Journal of proteome research, 20(4)},
-#'   1972–1980. \url{https://doi.org/10.1021/acs.jproteome.0c00602}
+#'   1972-1980. \url{https://doi.org/10.1021/acs.jproteome.0c00602}
 #'
 #' @importFrom dplyr select mutate filter rename %>% distinct
 #' @importFrom rlang sym