Make error more informative

bbimber · bbimber · commit a9b9fe901bae · 2022-02-03T07:00:22.000-08:00
diff --git a/singlecell/resources/chunks/RunCellHashing.R b/singlecell/resources/chunks/RunCellHashing.R
@@ -12,12 +12,12 @@ for (datasetId in names(seuratObjects)) {
 
             fractionFailedHashing <- 1 - (sum(seuratObj@meta.data$HTO.Classification %in% c('Singlet', 'Doublet')) / nrow(seuratObj@meta.data))
             if (!is.null(maxHashingPctFail) && fractionFailedHashing > maxHashingPctFail) {
-                addErrorMessage(paste0('Fraction failing cell hashing was : ', fractionFailedHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctFail))
+                addErrorMessage(paste0('Fraction failing cell hashing was : ', fractionFailedHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctFail, '. Total cells: ', nrow(seuratObj@meta.data)))
             }
 
             fractionDiscordantHashing <- sum(seuratObj@meta.data$HTO.Classification == 'Discordant') / nrow(seuratObj@meta.data)
             if (!is.null(maxHashingPctDiscordant) && fractionDiscordantHashing > maxHashingPctDiscordant) {
-                addErrorMessage(paste0('Discordant hashing rate was: ', fractionDiscordantHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctDiscordant))
+                addErrorMessage(paste0('Discordant hashing rate was: ', fractionDiscordantHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctDiscordant, '. Total cells: ', nrow(seuratObj@meta.data)))
             }
         } else {
             # Add empty columns to keep objects consistent

Original file line number	Diff line number	Diff line change
`@@ -12,12 +12,12 @@ for (datasetId in names(seuratObjects)) {`
`12`	`12`
`13`	`13`	`fractionFailedHashing <- 1 - (sum(seuratObj@meta.data$HTO.Classification %in% c('Singlet', 'Doublet')) / nrow(seuratObj@meta.data))`
`14`	`14`	`if (!is.null(maxHashingPctFail) && fractionFailedHashing > maxHashingPctFail) {`
`15`		`- addErrorMessage(paste0('Fraction failing cell hashing was : ', fractionFailedHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctFail))`
	`15`	`+ addErrorMessage(paste0('Fraction failing cell hashing was : ', fractionFailedHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctFail, '. Total cells: ', nrow(seuratObj@meta.data)))`
`16`	`16`	`}`
`17`	`17`
`18`	`18`	`fractionDiscordantHashing <- sum(seuratObj@meta.data$HTO.Classification == 'Discordant') / nrow(seuratObj@meta.data)`
`19`	`19`	`if (!is.null(maxHashingPctDiscordant) && fractionDiscordantHashing > maxHashingPctDiscordant) {`
`20`		`- addErrorMessage(paste0('Discordant hashing rate was: ', fractionDiscordantHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctDiscordant))`
	`20`	`+ addErrorMessage(paste0('Discordant hashing rate was: ', fractionDiscordantHashing, ' for dataset: ', datasetId, ', above threshold of: ', maxHashingPctDiscordant, '. Total cells: ', nrow(seuratObj@meta.data)))`
`21`	`21`	`}`
`22`	`22`	`} else {`
`23`	`23`	`# Add empty columns to keep objects consistent`