Fix empty VCF check

workflow/scripts/report/NV_description.R

@@ -8,6 +8,22 @@ library(logger)
 log_threshold(INFO)
 
 
+empty_vcf <- function() {
+  tibble(
+    variant     = character(),
+    REGION      = character(),
+    ALT_FREQ    = numeric(),
+    GFF_FEATURE = character(),
+    synonimous  = character(),
+    POS         = numeric(),
+    ALT         = character(),
+    NV_class    = character(),
+    NV_colors   = character(),
+    group       = character()
+  )
+}
+
+
 # Import file with plots style
 source(snakemake@params[["design"]])
 
@@ -150,15 +166,7 @@ log_info("Plotting summary figure for whole genome")
 
 if (nrow(vcf) == 0) {
   log_warn("Whole-genome VCF has no rows")
-  vcf <- tibble(
-    variant     = character(),
-    REGION      = character(),
-    ALT_FREQ    = numeric(),
-    GFF_FEATURE = character(),
-    synonimous  = character(),
-    POS         = numeric(),
-    ALT         = character()
-  )
+  vcf <- empty_vcf()
 }
 
 variants <- vcf %>%
@@ -312,15 +320,7 @@ window_plot_spike <- window %>%
 
 if (nrow(vcf_spike) == 0) {
   log_warn("Spike VCF has no rows")
-  vcf_spike <- tibble(
-    variant     = character(),
-    REGION      = character(),
-    ALT_FREQ    = numeric(),
-    GFF_FEATURE = character(),
-    synonimous  = character(),
-    POS         = numeric(),
-    ALT         = character()
-  )
+  vcf_spike <- empty_vcf()
 }
 
 variants_spike <- vcf_spike %>%
@@ -387,6 +387,11 @@ figur_SNP_table <- vcf_snp %>%
     ) %>%
   ungroup()
 
+if (nrow(figur_SNP_table) == 0) {
+  log_warn("Filtered SNP table has no rows")
+  figur_SNP_table <- empty_vcf()
+}
+
 figur_SNP_time <- figur_SNP_table %>%
   ggplot() +
   aes(