pWGS formatting fixes (#385)

* Formatting fixes * Summary tweak * Update checksum * Extra formatting tweaks * Adjust padding * Adjust padding * Conditional page break * Syntax fix * no top margin * Adjust padding * no message * Adjust bottom margin * checksums update --------- Co-authored-by: Oumaima Hamza <[email protected]>
oicr-gsi · Apr 26, 2024 · d2a94e9 · d2a94e9
1 parent 8157f38
commit d2a94e9
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Showing 7 changed files with 25 additions and 23 deletions.
diff --git a/src/lib/djerba/mergers/gene_information_merger/gene_information_template.html b/src/lib/djerba/mergers/gene_information_merger/gene_information_template.html
@@ -6,7 +6,7 @@
 %>
 
 <!-- gene information -->
-<hr class="big-white-line" style="width: 100%; ; page-break-before:always;">
+<hr class="big-white-line" style="width: 100%; margin-top: 0; padding-top: 0; page-break-before: always;">
 ${html_builder().section_cells_begin("<h3>Gene<br>Descriptions</h3>", True)}
 
 

diff --git a/src/lib/djerba/plugins/pwgs/analysis/analysis_template.html b/src/lib/djerba/plugins/pwgs/analysis/analysis_template.html
@@ -16,20 +16,20 @@
             the number of detected sites in the plasma sample was statistically 
             compared to the number of detected sites in a healthy control cohort. 
             The number of SNVs of tumour origin 
-            detected in this plasma sample (detected sites: <strong>${html_builder.k_comma_format(results.get(constants.SITES_DETECTED))}</strong>) was
+            detected in this plasma sample was
              <strong>${results.get(constants.SIGNIFICANCE)} </strong>  
-             than in the control cohort (N=${results.get(constants.COHORT_N)}). Dataset detection cutoff is <strong>${html_builder.k_comma_format(results.get(constants.DATASET_DETECTION_CUTOFF))}</strong>. </p>
+             than in the control cohort (N=${results.get(constants.COHORT_N)}). </p>
             <table class="variants" style="width:100%">
                   <thead>
                         <th style=" width:16%">Reads Checked</th>
-                        <th style=" width:16%">Reads Detected</th>
-                        <th style=" width:20%">Detected:Checked Reads (%)</th>
+                        <th style=" width:16%">Mutant Reads Detected</th>
+                        <th style=" width:20%">Mutant/Checked Read Percentage</th>
                   </thead>
                   <tbody>
                         <tr>
                               <td>${html_builder.k_comma_format(results.get(constants.READS_CHECKED))}</td>
                               <td>${html_builder.k_comma_format(results.get(constants.READS_DETECTED))}</td>
-                              <td>${results.get(constants.TUMOUR_FRACTION_READS)}</td>
+                              <td>${results.get(constants.TUMOUR_FRACTION_READS)}%</td>
                         </tr>
                   </tbody>
             </table>

diff --git a/src/lib/djerba/plugins/pwgs/analysis/detection.plot.R b/src/lib/djerba/plugins/pwgs/analysis/detection.plot.R
@@ -17,7 +17,7 @@ get_mrd_stats <- function(results, pval_cutoff){
   zscore <- (results$noise[results$label == "THIS SAMPLE"] - mean(results$noise))/ sd(results$noise)
   pvalue <- pnorm(zscore,lower.tail=F)
   dataset_cutoff <- (qnorm(pval_cutoff,lower.tail = F) * sd(results$noise)) +  mean(results$noise[results$label == "CONTROLS"])
-  
+
   mrd_stats <- list(
     "zscore" = zscore,
     "pvalue" = pvalue,
@@ -59,6 +59,7 @@ mean_detection <- mrd_stats$mean_detection
 sites_checked  <- mrd_stats$sites_checked
 dataset_cutoff <- mrd_stats$dataset_cutoff
 
+
 ##plot
 rep_length = round(log(sites_checked,10),0)
 my_breaks <- rep(1:9, rep_length) * (10^rep(0:(rep_length-1), each = 9))
@@ -73,7 +74,7 @@ my_labels[14] <- "Sites Detected:"
 
 options(bitmapType='cairo')
 svg(paste(output_directory,"pWGS.svg",sep="/"), width = 5, height = 1)
-    
+
 ggplot(results[results$label == "CONTROLS",]) + 
     geom_boxplot(aes(x=0,y=noise,color=label,shape=label),width = 0.05, outlier.shape = NA) +
 
@@ -82,9 +83,9 @@ ggplot(results[results$label == "CONTROLS",]) +
 
     annotate( geom="segment", x = -0.1, xend=0.1, y=dataset_cutoff, yend=dataset_cutoff, colour = "gray") +
 
-    annotate(geom="text",y = dataset_cutoff,x=0,color="gray30",label="Detection Cutoff",  vjust = -4.5, size=2.5) +
+    annotate(geom="text",y = dataset_cutoff,x=0,color="gray30",label=paste("Detection Cutoff:", round(dataset_cutoff, 2),"reads"),  vjust = -4.5, size=2.5) +
     annotate(geom="text",y = mean_detection, x=0,color="black",label="Control Cohort", hjust = 0.3, vjust = 3, size=2.5) +
-    annotate(geom="text",y = results$sites_detected[1],x=0,color="red",label="This Sample",  vjust = -2.5,size=2.5) +
+    annotate(geom="text",y = results$sites_detected[1],x=0,color="red",label=paste("This Sample:",round(results$sites_detected[1]),"reads"),  vjust = -2.5,size=2.5) +
 
     annotate(geom="point",y = results$sites_detected[1],x=0,color="red",shape=1, size=5) +
     annotate(geom="point",y = results$sites_detected[1],x=0,color="red",shape=20, size=1.5) +

diff --git a/src/lib/djerba/plugins/pwgs/summary/summary_template.html b/src/lib/djerba/plugins/pwgs/summary/summary_template.html
@@ -8,7 +8,7 @@
       <div class="oneoftwocellmain"  >
           <h2 >Summary</h2>
       </div>
-      <div class="twooftwocellmain"  style="height: 80px; padding: 10px; background-color:rgba(194,194,194,.5);  border: 3px solid #65bc45; border-radius: 12px" >
+      <div class="twooftwocellmain"  style="height: 80px; padding: 10px; background-color:rgba(194,194,194,.5);  border: 3px solid; border-radius: 12px" >
           <hr class="big-line" style="margin-top: -30px;">
 
   <h3 style="margin-top: 45px;">Cell-free DNA tumour burden: ${results.get(constants.CTDNA_DETECTION)}</h3>

diff --git a/src/lib/djerba/plugins/supplement/body/resources/PWGS.definitions.html b/src/lib/djerba/plugins/supplement/body/resources/PWGS.definitions.html
@@ -17,6 +17,6 @@
   <br><strong>Candidate SNVs: </strong>the number of single nucleotide variants from the primary tumour that can be used for ctDNA detection. 
   If the number of candidate SNVs is too low (below 4,000), mutational sampling analysis is unreliable.
 
-  <br><strong>Detected-Checked Reads Ratio: </strong>the percentage of reads with primary tumour matches divided by the total checked reads covering candidate sites.
+  <br><strong>Mutant/Checked Read Percentage: </strong>the percentage of reads with primary tumour matches divided by the total checked reads covering candidate sites.
   When ctDNA is detected, it may be an estimate of the fraction of ctDNA in the blood, but if ctDNA is not detected, it is an estimate of sequencing artefact matches.
 </p>
diff --git a/src/lib/djerba/plugins/supplement/body/supplementary_materials_template.html b/src/lib/djerba/plugins/supplement/body/supplementary_materials_template.html
@@ -68,7 +68,7 @@
       <td width="33%">Report drafted by ${results.get(core_constants.AUTHOR)} on ${results.get('extract_date')}</td>
     </tr>
     <tr>
-      <td width="33%">Report electronically signed out by ${results.get('clinical_geneticist_name')} (ABMS #${results.get('clinical_geneticist_licence')}) on ${results.get('report_signoff_date')}</td>
+      <td width="33%" style="padding-bottom: ${'300px' if ASSAY == 'PWGS' else '0'};">Report electronically signed out by ${results.get('clinical_geneticist_name')} (ABMS #${results.get('clinical_geneticist_licence')}) on ${results.get('report_signoff_date')}</td>
     </tr>
   </table>
 
@@ -78,10 +78,10 @@
   ${html_builder().section_cells_end()}
 
 
-  <hr class="big-line" style="width: 100%; ; page-break-after:always;"  >
+  <hr class="big-line" style="width: 100%; ${'page-break-after: always;' if ASSAY != 'PWGS' else ''}" >
   <hr class="header-big-line" style="width:100%; align:right">
 
-  <h2>APPENDIX</h2>
+<h2 >APPENDIX</h2>
 
   % if ASSAY in ('WGTS','TAR','WGS') and not FAILED:
 
@@ -96,7 +96,8 @@ <h2>APPENDIX</h2>
   <br/>
   <hr class="big-white-line" >
 
-  ${html_builder().section_cells_begin("<h3>Definitions</h3>",False)}
+  ${html_builder().section_cells_begin("<h3 style='margin-bottom: 0; padding-bottom: 0;'>Definitions</h3>", False)}
+
 
   % if not FAILED:
       % if ASSAY in ['WGTS', 'WGTS40X']:

diff --git a/src/lib/djerba/plugins/supplement/body/test/plugin_test.py b/src/lib/djerba/plugins/supplement/body/test/plugin_test.py
@@ -24,7 +24,7 @@ def testPwgsSupplementary(self):
         params = {
             self.INI: 'PWGS.supp.ini',
             self.JSON: json_location,
-            self.MD5: '878c2defac8b85e2ca9000fa13479d03'
+            self.MD5: '8a958cc5924b86cb05a0d8ea94fd34cb'
         }
         self.run_basic_test(test_source_dir, params)
 
@@ -34,7 +34,7 @@ def testTarSupplementary(self):
         params = {
             self.INI: 'TAR.supp.ini',
             self.JSON: json_location,
-            self.MD5: '4ff388fc36cba071715101583eb467af'
+            self.MD5: 'c0068f1b1d35ccb5272ee0ad466dc7ef'
         }
         self.run_basic_test(test_source_dir, params)
 
@@ -44,7 +44,7 @@ def testTarFailSupplementary(self):
         params = {
             self.INI: 'TAR.FAIL.supp.ini',
             self.JSON: json_location,
-            self.MD5: 'b0b0c44835ff2055316f7df6408b8fa4'
+            self.MD5: '5826fffc01fed3f879620ba04c9bf722'
         }
         self.run_basic_test(test_source_dir, params)
 
@@ -54,7 +54,7 @@ def testWgtsSupplementary(self):
         params = {
             self.INI: 'WGTS.supp.ini',
             self.JSON: json_location,
-            self.MD5: 'bb7e1ce8b6af9fcd3003be6d8ad5f976'
+            self.MD5: '125e44dbed16df044a3fd61313888e84'
         }
         self.run_basic_test(test_source_dir, params)
 
@@ -64,7 +64,7 @@ def testWgtsFailSupplementary(self):
         params = {
             self.INI: 'WGTS.FAIL.supp.ini',
             self.JSON: json_location,
-            self.MD5: '56f3eb5c6c662cf67e8a4fb8ea219f09'
+            self.MD5: 'baf0e752b61c7176eaec06de9611e836'
         }
         self.run_basic_test(test_source_dir, params)
 
@@ -74,7 +74,7 @@ def testWgts40XSupplementary(self):
         params = {
             self.INI: 'WGTS40X.supp.ini',
             self.JSON: json_location,
-            self.MD5: '021ef28363c75a55b69ff9abd6167320'
+            self.MD5: '00657dd036c9793497156136284541c5'
         }
         self.run_basic_test(test_source_dir, params)
 
@@ -84,7 +84,7 @@ def testWgts40XFailSupplementary(self):
         params = {
             self.INI: 'WGTS40X.FAIL.supp.ini',
             self.JSON: json_location,
-            self.MD5: '42e54fe6c150806d8d884d2c762957a1'
+            self.MD5: '5c8e1e269d924e0d4cb3d1492480cbdc'
         }
         self.run_basic_test(test_source_dir, params)