From fdd308f30992c2d72c12ea4b71ea192f369a0c63 Mon Sep 17 00:00:00 2001 From: tonywu1999 Date: Thu, 24 Sep 2026 11:03:45 -0400 Subject: [PATCH 1/2] fix profile plot warning --- R/utils_dataprocess_plots.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/R/utils_dataprocess_plots.R b/R/utils_dataprocess_plots.R index 5036773a..f3cf7806 100644 --- a/R/utils_dataprocess_plots.R +++ b/R/utils_dataprocess_plots.R @@ -157,8 +157,7 @@ num_features = data.table::uniqueN(input$FEATURE) profile_plot = ggplot(data = input, aes(x = .data$RUN, y = .data$newABUNDANCE, - color = .data$analysis, linetype = .data$FEATURE, - size = .data$analysis)) + + color = .data$analysis, linetype = .data$FEATURE)) + facet_grid(~LABEL) + geom_line(linewidth = 0.5) From d8925cf8f0b1ffed626413dd30db7b7e94156091 Mon Sep 17 00:00:00 2001 From: tonywu1999 Date: Thu, 24 Sep 2026 15:02:02 -0400 Subject: [PATCH 2/2] backwards compatibility enable previous datasets without LABEL --- R/dataProcessPlots.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/dataProcessPlots.R b/R/dataProcessPlots.R index 76da2a7e..9a290729 100644 --- a/R/dataProcessPlots.R +++ b/R/dataProcessPlots.R @@ -391,7 +391,8 @@ dataProcessPlots = function( Protein == all_proteins[i], list(PROTEIN = unique(Protein), PEPTIDE = "Run summary", TRANSITION = "Run summary", FEATURE = "Run summary", - LABEL = raw_label_map[LABEL], RUN = RUN, + LABEL = if("LABEL" %in% names(.SD)) raw_label_map[LABEL] else "Endogenous", + RUN = RUN, ABUNDANCE = LogIntensities, FRACTION = 1, UPPERBOUND = if("Variance" %in% names(.SD)) LogIntensities + 1.96 * sqrt(Variance) else NA_real_, # 95% confidence interval LOWERBOUND = if("Variance" %in% names(.SD)) LogIntensities - 1.96 * sqrt(Variance) else NA_real_