Add flags to reports

reports/report.Rmd

@@ -43,8 +43,7 @@ GREEN <- "#28a745"
 ORANGE <- "#ff8800"
 
 link_to_sample <- function(sample) {
-  return (sample)
-  #paste0('<a target=_blank href=samples/', sample, '.html>', sample,'</a>' )
+  paste0('<a target=_blank href="samples/', sample, '.html">', sample,'</a>' )
 }
 
 
@@ -100,14 +99,21 @@ contamination <- merge(contamination, mapping, by.x="Sample", by.y="Filename") %
 contaminated_samples = contamination %>%
   rename("Contamination_Status" = "Contamination.Status") %>%
   filter(Contamination_Status == "YES");
+#variants_count <- data.table(t(table(variants$ID)))
+#variants_count <- merge(variants_count, mapping, by.x="V2", by.y="Filename") %>%
+#  arrange(Sample_Label)
 
-variants_count <- data.table(t(table(variants$ID)))
-variants_count <- merge(variants_count, mapping, by.x="V2", by.y="Filename") %>%
+variants <- merge(variants, mapping, by.x="ID", by.y="Filename") %>%
   arrange(Sample_Label)
 
-variants <- merge(variants, mapping, by.x="ID", by.y="Filename") %>%
+variants_count <- variants %>% group_by(Sample_Label) %>% 
+  summarise(
+    N = n(),
+    Filtered = sum(Filter != "PASS")
+  ) %>%
   arrange(Sample_Label)
 
+
 variant_caller <- pipeline_params %>%
   filter(Parameter == "Variant Caller")
 
@@ -296,9 +302,9 @@ Row
 ```{r}
 variants_count %>%
   mutate (Sample_Link = link_to_sample(Sample_Label)) %>%
-  select("Sample_Link", "N") %>%
+  select("Sample_Link", "N", "Filtered") %>%
   datatable(
-    colnames=c("Sample", "Number of Variants"),
+    colnames=c("Sample", "Number of Variants", "Flagged Variants"),
     options = list(
       bPaginate = FALSE
     ),

reports/sample.Rmd

@@ -133,6 +133,10 @@ variants <- variants %>%
     Type == 2 ~ create_label('Heteroplasmy', 'default'),
     Type == 3 ~ create_label('InDel', 'info'),
     TRUE ~ "Unknown"
+  )) %>%
+  mutate(Filter_Label = case_when(
+    Filter == "PASS" ~ create_label('PASS', 'success'),
+    TRUE ~ create_label(Filter, 'warning')
   ))
 
 variant_caller <- pipeline_params %>%
@@ -182,19 +186,40 @@ statistics %>%
 #)
 ```
 
+### Variant Flags
+
+```{r}
+variants %>% count(Filter_Label) %>%
+  datatable(
+    colnames=c("Filter Flag", "Variants"),
+    options = list(
+      bPaginate = FALSE,
+      bFilter = FALSE,
+      bSort = FALSE,
+      bFooter = FALSE,
+      info = FALSE
+    ),
+    escape = FALSE,
+    rownames = FALSE,
+    class = 'cell-border stripe'
+  )
+  
+```
+
 ### Variants and Hetroplasmies
 
 Detected **`r variants %>% filter(Type == 1) %>% nrow()` variants**, **`r variants %>% filter(Type == 2) %>% nrow()` heteroplasmies** and **`r  variants %>% filter(Type == 3) %>% nrow()` InDels**.
 
+
 ```{r}
 variants %>% 
   mutate(
     Variant_Label = link_to_variant(Pos, Ref, Variant)
   ) %>% 
   arrange(Pos, Ref, Variant) %>%
-  select("Variant_Label", "VariantLevel", "Type_Label") %>%
+  select("Variant_Label", "VariantLevel", "Type_Label","Filter_Label") %>%
   datatable(
-    colnames=c("Variant", "Level", ""),
+    colnames=c("Variant", "Level", "Type","Flags"),
     options = list(
       bPaginate = FALSE,
       bFilter = FALSE,