Merge pull request #165 from MoTrPAC/develop

v0.7.4: general improvements
MoTrPAC · Oct 9, 2022 · 2ca2e6a · 2ca2e6a
2 parents d320ae7 + d633139
commit 2ca2e6a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MotrpacBicQC
 Type: Package
 Title: QC/QA functions for the MoTrPAC community
-Version: 0.7.3
-Date: 2022-10-02
+Version: 0.7.4
+Date: 2022-10-09
 Author: MoTrPAC Bioinformatics Center
 Maintainer: David Jimenez-Morales <davidjm@stanford.edu>
 Description: R Package for the analysis of MoTrPAC datasets. 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# MotrpacBicQC 0.7.4 (2022-10-09)
+
+* Metabolomics plots: check if enough compounds to generate plots
+* Update `assay_codes`: conventional assays code added (CONV)
+
 # MotrpacBicQC 0.7.3 (2022-10-02)
 
 * Adjustments to generate data releases (deal with pass1a/1c)

diff --git a/R/metabolomics_plots.R b/R/metabolomics_plots.R
@@ -52,7 +52,7 @@ plot_basic_metabolomics_qc <- function(results,
   # Density plots------ 
 
   if(verbose) message("       - (p) Density distributions")
-  mu <- results_long %>% group_by(sample_id) %>% summarise(grp.mean=mean(intensity))
+  mu <- results_long %>% group_by(sample_id) %>% dplyr::summarise(grp.mean=mean(intensity))
 
   den1 <- ggplot(data = results_long, aes(x = log2(intensity), color = sample_type)) + 
     geom_density(na.rm = TRUE) + 
@@ -319,6 +319,20 @@ plot_basic_metabolomics_qc <- function(results,
   out_plot_large <- file.path(normalizePath(out_qc_folder), paste0(output_prefix,"-qc-basic-large-plots.pdf"))
   out_plot_summary <- file.path(normalizePath(out_qc_folder), paste0(output_prefix,"-qc-basic-summary-plots.pdf"))
 
+  .plotThePlots <- function(theplot, verbose = TRUE) {
+    tryCatch(
+      {
+        print(theplot)
+      },
+      error=function(cond) {
+        if(verbose) message("       - Plot cannot be printed")
+
+      },
+      warning=function(cond) {
+        if(verbose) message(paste("       - Print density plots cause warnings"))
+      })
+  }
+
   if(printPDF){
     if(sn > 800){
       pdf(out_plot_large, width = 40, height = 8)
@@ -328,20 +342,20 @@ plot_basic_metabolomics_qc <- function(results,
       pdf(out_plot_large, width = 14, height = 8)
     }
   }
-  print(psumint)
-  print(puid1)
-  print(piseio)
+  .plotThePlots(psumint)
+  .plotThePlots(puid1)
+  .plotThePlots(piseio)
   gridExtra::grid.arrange(piseso, puid2, ncol = 1, heights = c(2, 1))
-  print(p_na_peprii)
+  .plotThePlots(p_na_peprii)
   if(printPDF) garbage <- dev.off()
 
   if(printPDF) pdf(out_plot_summary, width = 12, height = 6)
-  print(ptns)
+  .plotThePlots(ptns)
   gridExtra::grid.arrange(ppids, pnids, ncol = 2)
-  print(den1)
-  print(den2)
-  print(den3)
-  if(!is.null(metametab)){print(pmzrt)}
+  .plotThePlots(den1)
+  .plotThePlots(den2)
+  .plotThePlots(den3)
+  if(!is.null(metametab)){.plotThePlots(pmzrt)}
   if(printPDF) garbage <- dev.off()
 }
 

diff --git a/R/metabolomics_qc.R b/R/metabolomics_qc.R
@@ -744,37 +744,42 @@ validate_metabolomics <- function(input_results_folder,
         # This is targeted (no unnamed metabolites, no mz/rt plots)
         results <- r_m_n[eresults_coln]
       }
-
-      # results: check for negative values
-      results_long <- results %>% tidyr::pivot_longer(cols = -c(metabolite_name, id_type),
-                                                      names_to = "sample_id",
-                                                      values_to = "intensity")
-
-      results_long <- merge(m_s_n, results_long, by = c("sample_id"))
-      results_long$sample_id <- as.character(results_long$sample_id)
-      results_long$sample_id <- as.factor(results_long$sample_id)
-      results_long$sample_type <- as.factor(results_long$sample_type)
-      results_long <- results_long[which(results_long$intensity != 0),]
-      results_long <- results_long[!is.na(results_long$intensity),]
-      if(any(results_long$intensity < 0)){
-        message("   - (-) !!!!!!!!!!!!!!!!!!!!!!!!!!")
-        message("   - (-) NEGATIVE VALUES DETECTED!! ")
-        message("   - (-) !!!!!!!!!!!!!!!!!!!!!!!!!!")
-        results_long <- results_long[which(results_long$intensity > 0),]
-        ic <- ic + 1
+      # Ensure there are enough compounds to generate plots
+      if(dim(results)[1] > 1){
+        # results: check for negative values
+        results_long <- results %>% tidyr::pivot_longer(cols = -c(metabolite_name, id_type),
+                                                        names_to = "sample_id",
+                                                        values_to = "intensity")
+
+        results_long <- merge(m_s_n, results_long, by = c("sample_id"))
+        results_long$sample_id <- as.character(results_long$sample_id)
+        results_long$sample_id <- as.factor(results_long$sample_id)
+        results_long$sample_type <- as.factor(results_long$sample_type)
+        results_long <- results_long[which(results_long$intensity != 0),]
+        results_long <- results_long[!is.na(results_long$intensity),]
+        if(any(results_long$intensity < 0)){
+          message("   - (-) !!!!!!!!!!!!!!!!!!!!!!!!!!")
+          message("   - (-) NEGATIVE VALUES DETECTED!! ")
+          message("   - (-) !!!!!!!!!!!!!!!!!!!!!!!!!!")
+          results_long <- results_long[which(results_long$intensity > 0),]
+          ic <- ic + 1
+        }
+
+        plot_basic_metabolomics_qc(results = results, 
+                                   results_long = results_long,
+                                   metametab = metametab, 
+                                   out_qc_folder = out_qc_folder, 
+                                   output_prefix = output_prefix,
+                                   printPDF = printPDF,
+                                   untargeted = untargeted,
+                                   verbose = verbose)
+
+      }else{
+        message("  (-) QC plots are not possible: not enough compounds")
       }
-
-      plot_basic_metabolomics_qc(results = results, 
-                                 results_long = results_long,
-                                 metametab = metametab, 
-                                 out_qc_folder = out_qc_folder, 
-                                 output_prefix = output_prefix,
-                                 printPDF = printPDF,
-                                 untargeted = untargeted,
-                                 verbose = verbose)
 
     }else{
-      message("\n- (-) QC plots are not possible: critical datasets are missed")
+      if(verbose) message("\n- (-) QC plots are not possible: critical datasets are missed")
     }
 
     if(f_rmn & f_mmn){

diff --git a/data/assay_codes.rda b/data/assay_codes.rda
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2022-10-02">
+<meta name="date" content="2022-10-09">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.16/header-attrs.js"></script><script src="other_functions_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="other_functions_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -123,7 +123,7 @@ <h1 class="title">MotrpacBicQC: Other Functions</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-09</p>
 
 
 

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2022-10-02">
+<meta name="date" content="2022-10-09">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.16/header-attrs.js"></script><script src="qc_metabolomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_metabolomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Metabolomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-09</p>
 
 
 

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2022-10-02">
+<meta name="date" content="2022-10-09">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.16/header-attrs.js"></script><script src="qc_proteomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_proteomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Proteomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-02</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-10-09</p>
 
 
 

diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/notes_developers.html b/docs/notes_developers.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   other_functions: other_functions.html
   qc_metabolomics: qc_metabolomics.html
   qc_proteomics: qc_proteomics.html
-last_built: 2022-10-03T05:32Z
+last_built: 2022-10-09T07:07Z
 
diff --git a/docs/reference/assay_abbr.html b/docs/reference/assay_abbr.html
diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html
diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html
diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html
diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html
diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html
diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html
diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html
diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html
diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html