Add function for feature prioritization

DESCRIPTION

@@ -53,9 +53,11 @@ Imports:
     glue,
     graphics,
     grDevices,
-    jsonlite,
     hardhat,
+    igraph,
+    jsonlite,
     methods,
+    networkD3,
     parsnip,
     purrr,
     patchwork,
@@ -89,4 +91,4 @@ biocViews:
     Visualization
 URL: https://github.com/JRaviLab/amRml
 BugReports: https://github.com/JRaviLab/amRml/issues
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -2,8 +2,25 @@
 
 export(.getTargetVarName)
 export(applyBenjaminiHochberg)
+export(buildFeatureNetwork)
 export(buildLRModel)
+export(buildPerfPq)
+export(buildPerfPqCrossCountry)
+export(buildPerfPqCrossDrug)
+export(buildPerfPqCrossYear)
+export(buildPerfPqLOOCountry)
+export(buildPerfPqLOODrug)
+export(buildPerfPqLOOYear)
+export(buildPerfPqMDR)
+export(buildPerfPqYearCountry)
+export(buildPredPqMDR)
 export(buildRecipe)
+export(buildTopFeatsPq)
+export(buildTopFeatsPqLOOCountry)
+export(buildTopFeatsPqLOODrug)
+export(buildTopFeatsPqLOOYear)
+export(buildTopFeatsPqMDR)
+export(buildTopFeatsPqYearCountry)
 export(buildTuningGrid)
 export(buildWflow)
 export(calculateEvalMets)
@@ -13,16 +30,20 @@ export(createMLResultDir)
 export(createMLinputList)
 export(encodePhenotype)
 export(extractTopFeats)
+export(findSharedClusters)
+export(findUniqueClusters)
 export(fitBestModel)
 export(generateMLInputs)
 export(getConfusionMatrix)
 export(getNumFeat)
 export(loadMLInputTibble)
+export(parse_ml_filename)
 export(plotBaselineComparison)
 export(plotCM)
 export(plotCrossDrug)
 export(plotDrugDist)
 export(plotDrugPerf)
+export(plotFeatureNetworkD3)
 export(plotFishers)
 export(plotMDR)
 export(plotPRC)
@@ -43,6 +64,8 @@ export(runModelingPipeline)
 export(selectBestModel)
 export(shuffleLabels)
 export(splitMLInputTibble)
+export(summariseClusters)
+export(topFeaturesPerDrugOrClass)
 export(tuneGrid)
 import(arrow)
 import(dplyr)
@@ -51,116 +74,154 @@ import(ggrepel)
 import(purrr)
 import(stringr)
 import(tibble)
-importFrom(DBI,dbConnect)
-importFrom(DBI,dbDisconnect)
-importFrom(DBI,dbExecute)
-importFrom(DBI,dbGetQuery)
-importFrom(DBI,dbWriteTable)
-importFrom(arrow,read_parquet)
-importFrom(arrow,write_parquet)
-importFrom(dplyr,all_of)
-importFrom(dplyr,arrange)
-importFrom(dplyr,bind_rows)
-importFrom(dplyr,case_when)
-importFrom(dplyr,count)
-importFrom(dplyr,desc)
-importFrom(dplyr,distinct)
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,if_any)
-importFrom(dplyr,matches)
-importFrom(dplyr,mutate)
-importFrom(dplyr,n_distinct)
-importFrom(dplyr,pull)
-importFrom(dplyr,relocate)
-importFrom(dplyr,rename)
-importFrom(dplyr,row_number)
-importFrom(dplyr,rowwise)
-importFrom(dplyr,select)
-importFrom(dplyr,slice)
-importFrom(dplyr,summarise)
-importFrom(dplyr,ungroup)
+importFrom(DBI,
+  dbConnect,
+  dbDisconnect,
+  dbExecute,
+  dbGetQuery,
+  dbWriteTable
+)
+importFrom(arrow,
+  read_parquet,
+  write_parquet
+)
+importFrom(dplyr,
+  all_of,
+  arrange,
+  bind_rows,
+  case_when,
+  count,
+  desc,
+  distinct,
+  filter,
+  group_by,
+  if_any,
+  matches,
+  mutate,
+  n_distinct,
+  pull,
+  relocate,
+  rename,
+  row_number,
+  rowwise,
+  select,
+  slice,
+  summarise,
+  ungroup
+)
 importFrom(duckdb,duckdb)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,element_blank)
-importFrom(ggplot2,element_line)
-importFrom(ggplot2,element_text)
-importFrom(ggplot2,geom_line)
-importFrom(ggplot2,geom_path)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,theme)
-importFrom(ggplot2,xlab)
-importFrom(ggplot2,ylim)
+importFrom(ggplot2,
+  aes,
+  element_blank,
+  element_line,
+  element_text,
+  geom_line,
+  geom_path,
+  geom_point,
+  ggplot,
+  labs,
+  theme,
+  xlab,
+  ylim
+)
 importFrom(glmnet,glmnet)
 importFrom(glue,glue)
 importFrom(grDevices,colorRampPalette)
 importFrom(graphics,barplot)
 importFrom(hardhat,tune)
-importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,write_json)
+importFrom(jsonlite,
+  fromJSON,
+  write_json
+)
 importFrom(methods,is)
-importFrom(parsnip,augment)
-importFrom(parsnip,boost_tree)
-importFrom(parsnip,extract_fit_engine)
-importFrom(parsnip,fit)
-importFrom(parsnip,logistic_reg)
-importFrom(parsnip,multinom_reg)
-importFrom(parsnip,rand_forest)
-importFrom(parsnip,set_engine)
-importFrom(parsnip,set_mode)
-importFrom(purrr,imap_dfr)
-importFrom(purrr,map)
-importFrom(purrr,map_int)
-importFrom(purrr,pmap_chr)
-importFrom(purrr,walk)
+importFrom(parsnip,
+  augment,
+  boost_tree,
+  extract_fit_engine,
+  fit,
+  logistic_reg,
+  multinom_reg,
+  rand_forest,
+  set_engine,
+  set_mode
+)
+importFrom(purrr,
+  imap_dfr,
+  map,
+  map_int,
+  pmap_chr,
+  walk
+)
 importFrom(readr,write_lines)
-importFrom(recipes,all_predictors)
-importFrom(recipes,recipe)
-importFrom(recipes,step_normalize)
-importFrom(recipes,step_pca)
-importFrom(recipes,step_zv)
-importFrom(recipes,update_role)
-importFrom(rlang,":=")
-importFrom(rlang,eval_tidy)
-importFrom(rlang,sym)
-importFrom(rsample,initial_split)
-importFrom(rsample,initial_validation_split)
-importFrom(rsample,testing)
-importFrom(rsample,training)
-importFrom(rsample,validation_set)
-importFrom(rsample,vfold_cv)
-importFrom(stats,coef)
-importFrom(stats,fisher.test)
-importFrom(stats,median)
-importFrom(stats,reformulate)
-importFrom(stats,reorder)
-importFrom(stats,sd)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_split)
-importFrom(tibble,add_column)
-importFrom(tibble,is_tibble)
-importFrom(tibble,tibble)
-importFrom(tidyr,drop_na)
-importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
-importFrom(tune,control_grid)
-importFrom(tune,extract_fit_parsnip)
-importFrom(tune,finalize_workflow)
-importFrom(tune,select_best)
-importFrom(tune,tune_grid)
-importFrom(vip,vi)
-importFrom(vip,vip)
-importFrom(workflows,add_model)
-importFrom(workflows,add_recipe)
-importFrom(workflows,workflow)
-importFrom(workflowsets,extract_fit_parsnip)
-importFrom(workflowsets,extract_spec_parsnip)
-importFrom(yardstick,bal_accuracy)
-importFrom(yardstick,conf_mat)
-importFrom(yardstick,f_meas)
-importFrom(yardstick,mcc)
-importFrom(yardstick,metric_set)
-importFrom(yardstick,pr_auc)
-importFrom(yardstick,pr_curve)
+importFrom(recipes,
+  all_predictors,
+  recipe,
+  step_normalize,
+  step_pca,
+  step_zv,
+  update_role
+)
+importFrom(rlang,
+  ":=",
+  eval_tidy,
+  sym
+)
+importFrom(rsample,
+  initial_split,
+  initial_validation_split,
+  testing,
+  training,
+  validation_set,
+  vfold_cv
+)
+importFrom(stats,
+  coef,
+  fisher.test,
+  median,
+  reformulate,
+  reorder,
+  sd
+)
+importFrom(stringr,
+  str_remove,
+  str_split
+)
+importFrom(tibble,
+  add_column,
+  is_tibble,
+  tibble
+)
+importFrom(tidyr,
+  drop_na,
+  pivot_longer,
+  pivot_wider
+)
+importFrom(tune,
+  control_grid,
+  extract_fit_parsnip,
+  finalize_workflow,
+  select_best,
+  tune_grid
+)
+importFrom(vip,
+  vi,
+  vip
+)
+importFrom(workflows,
+  add_model,
+  add_recipe,
+  workflow
+)
+importFrom(workflowsets,
+  extract_fit_parsnip,
+  extract_spec_parsnip
+)
+importFrom(yardstick,
+  bal_accuracy,
+  conf_mat,
+  f_meas,
+  mcc,
+  metric_set,
+  pr_auc,
+  pr_curve
+)

R/data.R

@@ -1,24 +1,38 @@
-#' Demo ML input tibble
-#'
-#' Stratified subset (30 Resistant + 30 Susceptible) of the AMP-genes-binary
-#' matrix from the bundled `Sfl_parquet.duckdb`, restricted to 80 feature
-#' columns.
-#'
-#' @format A tibble with 60 rows and 82 columns: `genome_id`,
-#'   `genome_drug.resistant_phenotype`, and 80 binary feature columns.
-#' @source `inst/scripts/make_demo_data.R`.
-#' @examples
-#' data(demo_ml_tibble)
-#' dim(demo_ml_tibble)
-"demo_ml_tibble"
+# FLAG for Abhirupa: data/demo_fit.rda and data/demo_ml_tibble.rda were
+# deleted in b8f45b1 ("Add example data and remove old, unused data"), but
+# the roxygen docs below (and @examples in plot_ml.R, run_ml_pipeline.R,
+# ife_ml.R, core_ml.R that call data(demo_ml_tibble)) still reference them.
+# Confirmed via `exists("demo_ml_tibble")` after devtools::load_all() -> FALSE,
+# the object genuinely isn't in the package anymore, so devtools::document()
+# fatally errors trying to build .Rd files for data that doesn't exist ('demo_ml_tibble'
+# is not an exported object from 'namespace:amRml'). Commented out both blocks
+# below as the minimal unblock so NAMESPACE regeneration can proceed for the
+# rest of the package. The real question -- restore the .rda files via
+# inst/scripts/make_demo_data.R, or retire these two blocks + the four
+# @examples blocks elsewhere that still call data(demo_ml_tibble) -- is still
+# open and needs her call; nothing below was deleted, just disabled.
 
-#' Demo LR fit
-#'
-#' A tuned logistic-regression workflow fitted on [demo_ml_tibble].
-#'
-#' @format A fitted `workflow` object (output of [fitBestModel()]).
-#' @source `inst/scripts/make_demo_data.R`.
-#' @examples
-#' data(demo_fit)
-#' class(demo_fit)
-"demo_fit"
+# #' Demo ML input tibble
+# #'
+# #' Stratified subset (30 Resistant + 30 Susceptible) of the AMP-genes-binary
+# #' matrix from the bundled `Sfl_parquet.duckdb`, restricted to 80 feature
+# #' columns.
+# #'
+# #' @format A tibble with 60 rows and 82 columns: `genome_id`,
+# #'   `genome_drug.resistant_phenotype`, and 80 binary feature columns.
+# #' @source `inst/scripts/make_demo_data.R`.
+# #' @examples
+# #' data(demo_ml_tibble)
+# #' dim(demo_ml_tibble)
+# "demo_ml_tibble"
+#
+# #' Demo LR fit
+# #'
+# #' A tuned logistic-regression workflow fitted on `demo_ml_tibble`.
+# #'
+# #' @format A fitted `workflow` object (output of [fitBestModel()]).
+# #' @source `inst/scripts/make_demo_data.R`.
+# #' @examples
+# #' data(demo_fit)
+# #' class(demo_fit)
+# "demo_fit"