Fixed error (variables not existing) when none of FSM, ISM, NIC or NN…

…C where present
ConesaLab · Sep 18, 2024 · 43070e3 · 43070e3
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commit 43070e3
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Showing 3 changed files with 51 additions and 42 deletions.
diff --git a/utilities/report_qc/SQANTI3_report.R b/utilities/report_qc/SQANTI3_report.R
@@ -2038,7 +2038,7 @@ if (nrow(data.junction) > 0 && nrow(x) > 0){
     t3.RTS <- rbind(t3.RTS, c("ISM", TRUE, 0,0,0,"RT switching"))
   }
   if(!("NIC" %in% t3.RTS$structural_category)){
-    t3.RTS <- rbind(t3.RTS, c("NIC", TRUE, ,0,0,"RT switching"))
+    t3.RTS <- rbind(t3.RTS, c("NIC", TRUE, 0,0,0,"RT switching"))
   }
   if(!("NNC" %in% t3.RTS$structural_category)){
     t3.RTS <- rbind(t3.RTS, c("NNC", TRUE,0,0,"RT switching"))
@@ -2252,37 +2252,37 @@ if (nrow(data.junction) > 0 && nrow(x) > 0){
     t3.a <- rbind(t3.annot[,c(1,5,6)], t3.a.SJ[,c(1,5,6)], t3.a.Cov[,c(1,5,6)])
 
   }
-
-}
-
-# Check if t3.SJ is not empty
-if (nrow(t3.SJ) > 0) {
-  t3.aa <-  rbind(t3.annot[,c("structural_category", "perc", "Var")], t3.a.SJ[,c(1,5,6)])
-
-  for(i in 1:length(t3.list)){
-    set=data.frame(t3.data.sets[i])
-    c=data.frame(t3.list[i])
-    if (!all(is.na(set))){
-      t.temp=t3.aa
-      t3.aa = rbind(t.temp, c[,c(1,5,6)])
+  # Check if t3.SJ is not empty
+  if (nrow(t3.SJ) > 0) {
+    t3.aa <-  rbind(t3.annot[,c("structural_category", "perc", "Var")], t3.a.SJ[,c(1,5,6)])
+
+    for(i in 1:length(t3.list)){
+      set=data.frame(t3.data.sets[i])
+      c=data.frame(t3.list[i])
+      if (!all(is.na(set))){
+        t.temp=t3.aa
+        t3.aa = rbind(t.temp, c[,c(1,5,6)])
+      }
     }
+
+    p28.a <- ggplot(data=t3.aa, aes(x=structural_category, y=perc, fill= Var)) +
+      geom_bar(position = position_dodge(), stat="identity", width = 0.7,  size=0.3, color="black") +
+      guides(fill=guide_legend(nrow=2,byrow=TRUE)) +
+      scale_fill_manual(values = c(myPalette)) +
+      scale_y_continuous(expand = expansion(mult = c(0,0.1))) +
+      ylab("Transcripts, %") +
+      xlab("") +
+      mytheme +
+      theme(legend.position="bottom", axis.title.x = element_blank()) +
+      ggtitle( "Good Quality Control Attributes Across Structural Categories\n\n" ) +
+      theme(axis.text.y = element_text(size=10),
+            axis.text.x  = element_text(size=10))+
+      theme(legend.title = element_blank())
   }
-
-  p28.a <- ggplot(data=t3.aa, aes(x=structural_category, y=perc, fill= Var)) +
-    geom_bar(position = position_dodge(), stat="identity", width = 0.7,  size=0.3, color="black") +
-    guides(fill=guide_legend(nrow=2,byrow=TRUE)) +
-    scale_fill_manual(values = c(myPalette)) +
-    scale_y_continuous(expand = expansion(mult = c(0,0.1))) +
-    ylab("Transcripts, %") +
-    xlab("") +
-    mytheme +
-    theme(legend.position="bottom", axis.title.x = element_blank()) +
-    ggtitle( "Good Quality Control Attributes Across Structural Categories\n\n" ) +
-    theme(axis.text.y = element_text(size=10),
-          axis.text.x  = element_text(size=10))+
-    theme(legend.title = element_blank())
 }
 
+
+
 #TSS ratio
 data.ratio = rbind(data.refmatch[,c(6,48)], data.ISM[,c(6,48)])
 if (!all(is.na(data.ratio$ratio_TSS))){

diff --git a/utilities/report_qc/SQANTI3_report.Rmd b/utilities/report_qc/SQANTI3_report.Rmd
@@ -1173,7 +1173,7 @@ ggplotly(p28)%>%
 cat ('\n')
 ```
 
-```{r ,exists("p28.RTS")}
+```{r , eval = exists("p28.RTS")}
 cat("#### RT-switching {.tabset .tabset-fade }")
 ggplotly(p28.RTS)%>%
   layout(margin = list(r = 130)) %>%

diff --git a/utilities/report_qc/generatePDFreport.R b/utilities/report_qc/generatePDFreport.R
@@ -501,35 +501,43 @@ generatePDFreport = function()
 
   s <- textGrob("Features of Bad Quality", gp=gpar(fontface="italic", fontsize=17), vjust = 0)
   grid.arrange(s)
-  print(p28.RTS)
-  print(p28.SJ)
-  if (n_t3.SJ>0 & n_t3.RTS>0 & !all(is.na(data.class$min_cov))) {
-    print(p28.Cov)
+  if (exists("p28.RTS")){
+    print(p28.RTS)  
   }
-  if (n_t3.SJ>0 & n_t3.RTS>0 &!all(is.na(data.class$predicted_NMD))) {
-    print(p28.NMD)
-  }
-  if (n_t3.SJ>0 & n_t3.RTS>0) {
-    print(p28)
+  if (exists("p28.SJ")){
+    print(p28.SJ)  
   }
 
+  if(exists("n_t3.SJ") & exists("n_t3.RTS")){
+    if (n_t3.SJ>0 & n_t3.RTS>0 & !all(is.na(data.class$min_cov))) {
+      print(p28.Cov)
+    }
+    if (n_t3.SJ>0 & n_t3.RTS>0 &!all(is.na(data.class$predicted_NMD))) {
+      print(p28.NMD)
+    }
+    if (n_t3.SJ>0 & n_t3.RTS>0) {
+      print(p28)
+    }
+  }
   s <- textGrob("Features of Good Quality", gp=gpar(fontface="italic", fontsize=17), vjust = 0)
   grid.arrange(s)
   if (!all(is.na(data.class$dist_to_cage_peak))) {
     print(p28.a.Cage)
   }
-  print(p28.a.annot)
+  if(exists("p28.a.annot")){
+    print(p28.a.annot) 
+  }
 
-  if (!all(is.na(data.class$polyA_motif))) {
+  if (!all(is.na(data.class$polyA_motif)) && exists("p28.a.polyA")) {
     print(p28.a.polyA)
   }
-  print(p28.a.SJ)
+  if(exists("p28.a.SJ")){print(p28.a.SJ)}
 
   if (!all(is.na(data.class$min_cov)) && exists("p28.a.Cov")) {
     print(p28.a.Cov)
   }
 
-  if (nrow(t3.SJ) > 0) {
+  if (exists("t3.SJ") && nrow(t3.SJ) > 0) {
     print(p28.a)
   }
 
@@ -541,3 +549,4 @@ generatePDFreport = function()
 
   print("SQANTI3 report successfully generated!")
 }
+