Revision of qcscore_model_spe branch#64
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BenedettaBanzi
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Jul 23, 2026
BenedettaBanzi
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- Fixed some issues with QS computation with custom formula;
- updated QC functions documentation;
- added more customazable settings to plot functions;
- function name standardization to Quality Score (QScore);
- updated vignettes.
…lected metrics. Function name standardization to QScore. plotCellsFovs with distinct parameters for points and FOV number sizes. Updated documentation and vignettes.
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Pull request overview
This PR updates SpaceTrooper’s Quality Score (QS) APIs and documentation, including renaming/standardizing “QCScore” to “QScore”, expanding plot customization controls, and refreshing vignettes/man pages for the new interface.
Changes:
- Renames QS-related functions/outputs (e.g.,
computeQCScore()→computeQScore(),QC_score→QScore) and updates package docs/vignettes accordingly. - Adds/extends support for user-specified QS model formulas and updates QS model training/application documentation.
- Expands plotting customization parameters (e.g., point size/alpha and label sizes) and updates associated docs/vignettes.
Reviewed changes
Copilot reviewed 14 out of 32 changed files in this pull request and generated 15 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/SpaceTrooper_utilities.Rmd | Updates utilities vignette for QScore naming and adds custom-formula example. |
| vignettes/RNA_tutorial_vignette.rmd | Updates RNA tutorial to use renamed QS APIs and updated plotting args. |
| vignettes/Protein_tutorial_vignette.Rmd | Updates protein tutorial to use renamed QS APIs and updated plotting args. |
| README.md | Updates quickstart example to computeQScore()/computeQScoreFlags(). |
| R/spatialQCPlots.R | Adds plot customization parameters and refactors plotting function signatures. |
| R/readMerfish.R | Updates warning message wording for Quality Score terminology. |
| R/QC.R | Renames/updates QS computation pipeline, formula handling, model application helper, and extensive roxygen updates. |
| NEWS.md | Updates release notes for 1.1.8 changes. |
| NAMESPACE | Updates exports to new function names (adds .applyQScoreModel, swaps QCScore exports for QScore). |
| man/trainModel.Rd | Updates documentation wording for ridge logistic regression model fitting. |
| man/spatialPerCellQC.Rd | Updates parameter descriptions and expanded behavior documentation. |
| man/plotZoomFovsMap.Rd | Documents new plotZoomFovsMap arguments and naming. |
| man/plotCellsFovs.Rd | Documents new plotCellsFovs arguments and naming. |
| man/getModelFormula.Rd | Updates usage to metricList (but needs consistency fixes). |
| man/dot-computeXenMerTrainSet.Rd | Documentation wording update for internal helper. |
| man/dot-computeCosmxTrainSet.Rd | Documentation wording update for internal helper. |
| man/dot-computeCosmxProteinTrainSet.Rd | Documentation wording update for internal helper. |
| man/dot-computeBorderDistanceCosMx.Rd | Documentation wording updates for FOV terminology. |
| man/dot-checkSkw.Rd | Documentation wording update for internal helper. |
| man/dot-applyQScoreModel.Rd | Adds documentation for .applyQScoreModel() (example currently inconsistent with actual API). |
| man/computeTrainDF.Rd | Updates docs to QScore_train naming and other wording. |
| man/computeThresholdFlags.Rd | Updates docs wording and clarifies outputs. |
| man/computeSpatialOutlier.Rd | Updates docs wording and clarifies behavior. |
| man/computeQScoreFlags.Rd | Adds documentation for computeQScoreFlags(). |
| man/computeQScore.Rd | Adds documentation for computeQScore(). |
| man/computeQCScoreFlags.Rd | Removes deprecated/renamed QCScoreFlags man page. |
| man/computeQCScore.Rd | Removes deprecated/renamed computeQCScore man page. |
| man/computeOutliersQScore.Rd | Renames and updates outlier-computation documentation for QScore. |
| man/computeLambda.Rd | Updates usage to new signature (but needs argument/example consistency fixes). |
| man/checkOutliers.Rd | Updates docs wording and naming to Quality Score. |
| man/applyQCScoreModel.Rd | Removes deprecated/renamed applyQCScoreModel man page. |
| DESCRIPTION | Bumps version to 1.1.8. |
Files not reviewed (18)
- man/checkOutliers.Rd: Generated file
- man/computeLambda.Rd: Generated file
- man/computeQScore.Rd: Generated file
- man/computeQScoreFlags.Rd: Generated file
- man/computeSpatialOutlier.Rd: Generated file
- man/computeThresholdFlags.Rd: Generated file
- man/computeTrainDF.Rd: Generated file
- man/dot-applyQScoreModel.Rd: Generated file
- man/dot-checkSkw.Rd: Generated file
- man/dot-computeBorderDistanceCosMx.Rd: Generated file
- man/dot-computeCosmxProteinTrainSet.Rd: Generated file
- man/dot-computeCosmxTrainSet.Rd: Generated file
- man/dot-computeXenMerTrainSet.Rd: Generated file
- man/getModelFormula.Rd: Generated file
- man/plotCellsFovs.Rd: Generated file
- man/plotZoomFovsMap.Rd: Generated file
- man/spatialPerCellQC.Rd: Generated file
- man/trainModel.Rd: Generated file
Comments suppressed due to low confidence (4)
man/computeLambda.Rd:18
computeLambdadocumentation is inconsistent with the new signaturecomputeLambda(modelMatrix, trainDF): it still documents amodelFormulaargument and the examples callcomputeLambda(df_train, modform). This will mislead users and fail during example checks.
This issue also appears on line 39 of the same file.
man/computeLambda.Rd:42
- The example still uses the old API (
getModelFormula(metadata(spe)$formula_variables)andcomputeLambda(df_train, modform)), but the function signatures were updated. This example will error if executed.
vignettes/SpaceTrooper_utilities.Rmd:513 - The vignette currently tells users the
I(abs(log2AspectRatio) * as.numeric(dist_border < 50))term "must have spaces around the*and<operators". Requiring exact whitespace makes the API brittle and is easy for users to get wrong; it’s better to document that whitespace is irrelevant (and ensure the implementation normalizes it).
R/QC.R:369 computeLambda()docs still say it "constructs the design matrix via model.matrix()", but the function now takesmodelMatrixas an argument and no longer builds it internally. This makes the description misleading.
#' Internally, the function:
#' constructs the design matrix via \code{model.matrix()},
#' runs k-fold cross-validation of ridge logistic regression using `cv.glmnet` with `alpha = 0`,
#' extracts and returns `ridge_cv$lambda.min`.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
| df <- ctx$df; out_var <- ctx$out_var; tech <- ctx$tech | ||
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| train_df <- computeTrainDF(df, out_var, tech, verbose) | ||
| model_formula <- getModelFormula(names(out_var)) |
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This is a wrong suggestion. model_formula should be built ALWAYS using the computed variables contained in out_var, not just when modelFormula is null. out_var is the vector of metrics resulting from the checks made by .prepQCContext. If the number of outliers is not enough, that metric is automatically discarded from the vector
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| #' @param formulaVars A named character vector mapping variable names | ||
| #' (e.g. `"log2SignalDensity"`, `"Area_um"`, etc.) to their corresponding | ||
| #' outlier label columns, typically from | ||
| #' `metadata(spe)$formula_variables`. |
| out_var <- metricList | ||
| if ("log2AspectRatio" %in% out_var) { | ||
| out_var[grep("log2AspectRatio", out_var)] <- | ||
| "I(abs(log2AspectRatio) * as.numeric(dist_border<50))" |
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| #' spe_test <- applyQScoreModel( | ||
| #' spe=spe_test, | ||
| #' qcModel=qc_model, | ||
| #' scoreName="QC_score_transferred" | ||
| #' scoreName="QScore_transferred" | ||
| #' ) |
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| spe_test <- applyQScoreModel( | ||
| spe=spe_test, | ||
| qcModel=qc_model, | ||
| scoreName="QScore_transferred" | ||
| ) |
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| getModelFormula(metricList) | ||
| } | ||
| \arguments{ | ||
| \item{formulaVars}{A named character vector mapping variable names | ||
| (e.g. `"log2SignalDensity"`, `"Area_um"`, etc.) to their corresponding | ||
| outlier label columns, typically from | ||
| `metadata(spe)$formula_variables`.} |
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| #' `~(log2SignalDensity + Area_um + I(abs(log2AspectRatio) * as.numeric(dist_border < 50)) + log2Ctrl_total_ratio)^2`. | ||
| #' When user-provided, the formula must follow the same default syntax and | ||
| #' removed (or added) terms should be written exactly as in the default formula, | ||
| #' e.g. `I(abs(log2AspectRatio) * as.numeric(dist_border < 50))` must have spaces | ||
| #' around the `*` and `<` operators. |
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| computeQScore <- function(spe, bestLambda=NULL, modelFormula=NULL, verbose=FALSE) { | ||
| stopifnot(is(spe, "SpatialExperiment")) | ||
| if (dim(spe[,spe$total == 0])[2] != 0) { | ||
| warning(paste0(dim(spe[,spe$total == 0])[2], |
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| #' @param trainDF `data.frame` | ||
| #' A data frame for training that must include: | ||
| #' A data frame for QS model training that must include: | ||
| #' Predictor columns: All columns referenced in the formula returned by `getModelFormula()`. | ||
| #' `qscore_train` A binary (0/1) response vector to be modeled. | ||
| #' @param modelFormula `character` |
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| #' @description | ||
| #' Apply a previously trained QC score model to a new SpatialExperiment object. | ||
| #' Internal: applies a previously trained Quality Score model to a new SpatialExperiment object. | ||
| #' See details for important considerations when applying a model to a | ||
| #' different dataset. | ||
| #' @details |
Owner
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@copilot based on your review, provide possible solutions to the problems in a different PR, and add the old computeQCScore function with the .Deprecated instruction based on the bioconductor guidelines present here: |
Contributor
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@drighelli I've opened a new pull request, #65, to work on those changes. Once the pull request is ready, I'll request review from you. |
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