Enhance plotting functions and documentation by AbhirupaGhosh · Pull Request #8 · JRaviLab/amRml

AbhirupaGhosh · 2026-01-20T18:24:46Z

Updated documentation for plotPRC, plotROC, plotCM, plotDensity, and plotTopFeatsVI functions. Added new functions for plotting ROC curves, confusion matrices, and density of predicted class probabilities.

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Feature (adds or updates new capabilities)
Bug fix (fixes an issue).
Enhancement (adds functionality).
Breaking change (these changes would cause existing functionality to not work as expected).

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Updated documentation for plotPRC, plotROC, plotCM, plotDensity, and plotTopFeatsVI functions. Added new functions for plotting ROC curves, confusion matrices, and density of predicted class probabilities.

epbrenner

These work, but I'd strongly suggest that the import functions for the plots to natively include the tsv reading rather than requiring it.

Add functions to plot drug phenotype distribution, model performance, and cross-drug generalization heatmaps.

AbhirupaGhosh · 2026-06-02T14:03:14Z

These work, but I'd strongly suggest that the import functions for the plots to natively include the tsv reading rather than requiring it.

I have modified the function to input tsv.
I have added additional plotting functions based on my Staph poster and a few others. @eboyer221, please look through the plots to decide if anything can be adapted for the dashboard or generate an Rmd as the end product of amRml.

eboyer221 · 2026-06-04T17:29:50Z

@AbhirupaGhosh @jananiravi @amcim
I am currently reviewing these plots and working on adding them into the amRviz dashboard, along with an option to export them. Since plotCrossDrug() uses ComplexHeatmap, bringing that into amRviz will give us a Bioconductor dependency we need, which should help resolve the BiocCheck warning we have been hitting in that package.

jananiravi · 2026-06-23T21:31:00Z

+#' @return A heatmap (`ggplot2` object) showing the confusion matrix.
+#'
+#' @export
+plotCM <- function(test_data_plus_predictions_file) {


plotConfusion will seem odd?

jananiravi · 2026-06-23T21:32:00Z

+#' @param shuffled_label_results Output of `runMLPipeline(shuffle_labels = TRUE)`
 #'
-#' @importFrom graphics barplot
+#' @return A base R barplot comparing balanced accuracy across models.


why base R?

jananiravi · 2026-06-23T21:33:09Z

+        "#0F2A5A" # very dark for ~1
+      ),
+      values = scales::rescale(c(-1, 0, 0.85, 1)),
+      name = "Best MCC"


@AbhirupaGhosh including ties?

jananiravi · 2026-06-23T21:33:44Z

+  feat_pal <- c(
+    "args"     = "#56B4E9", # sky blue
+    "cogs"     = "#E69F00", # orange
+    "genes"    = "#009E73", # bluish green
+    "domains"  = "#F0E442", # yellow
+    "proteins" = "#CC79A7", # reddish purple
+    "struct"   = "#D55E00" # vermillion
+  )


not defined separately in a function -- so it's the same colors across plots/panels?

jananiravi · 2026-06-23T21:34:27Z

+  final_plot
+}
+
+#' Plot cross-drug generalization heatmap


unless I'm missing something

Suggested change

#' Plot cross-drug generalization heatmap

#' Plot cross-drug prediction as a heatmap

jananiravi · 2026-06-23T21:35:01Z

+  cross_drug <- arrow::read_parquet(file.path(cross_test_performance_path, "cross_drug_perf.parquet"))
+  performance <- arrow::read_parquet(file.path(drug_performance_path, "all_performance.parquet"))
+
+  ###################### CROSS DRUG Testing #############################


Suggested change

###################### CROSS DRUG Testing #############################

jananiravi · 2026-06-23T21:35:47Z

+    tibble::column_to_rownames("drug_or_class") |>
+    as.matrix()
+
+  row_order <- heatmap_df |>


drugs ordered by their classes?

jananiravi · 2026-06-23T21:37:21Z

+    ggplot2::labs(
+      title = if (year_or_country == "year") {
+        "Temporal performance by drug"
+      } else {
+        "Geographical performance by drug"


Suggested change

ggplot2::labs(

title = if (year_or_country == "year") {

"Temporal performance by drug"

} else {

"Geographical performance by drug"

ggplot2::labs(

title = if (year_or_country == "year") {

"Performance of AMR drug models with temporal holdouts"

} else {

"Performance of AMR drug models with geographical holdouts"

jananiravi · 2026-06-23T21:38:17Z

+#' )
+plotTopClusters <- function(top_feat_path = ".", cluster_feature_path = ".",
+                            protein_names_path = ".", top_n = 10) {
+  ################### Top features #########################


Suggested change

################### Top features #########################

amcim · 2026-06-30T18:41:28Z

I am not approving yet, but basically some of the additions I made in PR #23 were reverted. So I am taking the time now to resolve this. I re-added much of this necessary code, including adding more runnable examples, fixed some R CMD CHECK bugs, and more. Ill write some details on approval. I will be pushing changes that hopefully will resolve CI, and then will review the plotting functions functionality.

Enhance plotting functions and documentation

de2fc86

Updated documentation for plotPRC, plotROC, plotCM, plotDensity, and plotTopFeatsVI functions. Added new functions for plotting ROC curves, confusion matrices, and density of predicted class probabilities.

AbhirupaGhosh requested review from epbrenner and jananiravi January 20, 2026 18:25

AbhirupaGhosh self-assigned this Jan 20, 2026

epbrenner previously approved these changes Jan 20, 2026

View reviewed changes

Merge branch 'main' into plotting_ml_results

c882078

AbhirupaGhosh dismissed epbrenner’s stale review via c882078 January 21, 2026 06:31

Style code (GHA)

9486c55

AbhirupaGhosh marked this pull request as draft May 29, 2026 22:25

AbhirupaGhosh and others added 5 commits May 29, 2026 16:39

Refactor plot functions to accept file inputs

d3a97bf

Style code (GHA)

2418366

Implement drug performance plotting functions in plot_ml.R

f2eb43c

Add functions to plot drug phenotype distribution, model performance, and cross-drug generalization heatmaps.

Style code (GHA)

7ece644

Merge branch 'main' into plotting_ml_results

e818b35

AbhirupaGhosh requested review from amcim and eboyer221 June 2, 2026 14:00

AbhirupaGhosh marked this pull request as ready for review June 2, 2026 14:03

eboyer221 mentioned this pull request Jun 4, 2026

BiocCheck warning involving Bioconductor dependencies JRaviLab/amRviz#29

Open

Merge branch 'main' into plotting_ml_results

8050c96

jananiravi reviewed Jun 23, 2026

View reviewed changes

amcim mentioned this pull request Jun 24, 2026

Add LOO and cross-drug test matrix generation #19

Merged

11 tasks

amcim added 2 commits June 25, 2026 11:33

Merge remote-tracking branch 'origin/main' into plotting_ml_results

cb7c301

adding back pr 23 changes and more runnable examples

6a2787e

AbhirupaGhosh and others added 2 commits July 1, 2026 17:15

plot enhancements

7177ab2

Style code (GHA)

49fc7e0

	#' Plot cross-drug generalization heatmap
	#' Plot cross-drug prediction as a heatmap

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AbhirupaGhosh commented Jan 20, 2026

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AbhirupaGhosh commented Jun 2, 2026

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amcim commented Jun 30, 2026

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