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fix(MSstats+): Fix download analysis code #209

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tonywu1999 merged 2 commits into from
May 13, 2026
Merged

fix(MSstats+): Fix download analysis code #209

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56a039b
fix(MSstats+): Fix download analysis code
tonywu1999 May 13, 2026
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fix coderabbit feedback
tonywu1999 May 13, 2026
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40 changes: 33 additions & 7 deletions R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -961,13 +961,29 @@ library(MSstatsPTM)\n", sep = "")
codes = paste(codes, "data = data.table::fread(\"insert your MSstats scheme output from Spectronaut filepath\")\nannot_file = data.table::fread(\"insert your annotation filepath\")#Optional\n"
, sep = "")

codes = paste(codes, "data = SpectronauttoMSstatsFormat(data,
annotation = annot_file #Optional,
filter_with_Qvalue = TRUE, ## same as default
qvalue_cutoff = 0.01, ## same as default
fewMeasurements=\"remove\",
removeProtein_with1Feature = TRUE,
if (isTRUE(input$calculate_anomaly_scores)) {
codes = paste(codes, "run_order = data.table::fread(\"insert your run order CSV filepath (Run, Order columns)\")\n", sep = "")
codes = paste(codes, "data = SpectronauttoMSstatsFormat(data,
annotation = annot_file, #Optional
filter_with_Qvalue = ", input$q_val, ",
qvalue_cutoff = ", input$q_cutoff, ",
removeProtein_with1Feature = ", input$remove, ",
use_log_file = FALSE,
calculateAnomalyScores = TRUE,
runOrder = run_order,
anomalyModelFeatures = c(\"FG.ShapeQualityScore (MS2)\", \"FG.ShapeQualityScore (MS1)\", \"EGDeltaRT\"),
anomalyModelFeatureTemporal = c(\"mean_decrease\", \"mean_decrease\", \"dispersion_increase\"),
n_trees = 100,
max_depth = \"auto\",
numberOfCores = 1)\n", sep = "")
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} else {
codes = paste(codes, "data = SpectronauttoMSstatsFormat(data,
annotation = annot_file, #Optional
filter_with_Qvalue = ", input$q_val, ",
qvalue_cutoff = ", input$q_cutoff, ",
removeProtein_with1Feature = ", input$remove, ",
use_log_file = FALSE)\n", sep = "")
}
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}
else if(input$filetype == 'diann') {

Expand Down Expand Up @@ -1391,14 +1407,16 @@ preprocessDataCode <- function(qc_input,loadpage_input) {
code_n_feat = 'NULL'
}

sum_method = if (!is.null(qc_input$summaryMethod)) qc_input$summaryMethod else "TMP"

codes = paste(codes, "\n# use MSstats for protein summarization\n", sep = "")
codes = paste(codes, "summarized = MSstats::dataProcess(data,
normalization = \'", qc_input$norm,"\',\t\t\t\t
logTrans = ", as.numeric(qc_input$log),",\t\t\t\t
nameStandards = ", paste0("c('", paste(qc_input$names, collapse = "', '"), "')"), ",\t\t\t\t
featureSubset = \'", qc_input$features_used, "\',\t\t\t\t
n_top_feature = ", code_n_feat, ",\t\t\t\t
summaryMethod=\"TMP\",
summaryMethod=\"", sum_method, "\",
censoredInt=\'", qc_input$censInt, "\',\t\t\t\t
MBimpute=", qc_input$MBi, ",\t\t\t\t
remove50missing=", qc_input$remove50, ",\t\t\t\t
Expand All @@ -1411,6 +1429,14 @@ preprocessDataCode <- function(qc_input,loadpage_input) {
which.Protein = \"Enter Protein to Plot Here\",
summaryPlot = TRUE,
address = FALSE,isPlotly=TRUE)\n", sep="")

if (isTRUE(loadpage_input$calculate_anomaly_scores)) {
codes = paste(codes, "\n# Plot per-feature quality metrics (e.g. AnomalyScores) carried through from the converter\n", sep = "")
codes = paste(codes, "MSstats::MSstatsQualityMetricsPlot(data,
metric = \"AnomalyScores\",
which.Protein = \"Enter Protein to Plot Here\",
isPlotly = TRUE)\n", sep = "")
}
}

return(codes)
Expand Down
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