Fix typographic error

Author: ahmig

workflow/scripts/filter_tsv.R

@@ -34,7 +34,7 @@ log_info("Finding synonymous and non synonymous variants")
 # Adding synonymous variable
 data <- mutate(
   data,
-  synonimous = case_when(
+  SYNONYMOUS = case_when(
     REF_AA == ALT_AA ~ "Yes",
     TRUE ~ "No"
   )

workflow/scripts/report/NV_description.R

@@ -43,7 +43,7 @@ empty_vcf <- tibble(
   VARIANT_NAME = as.character(NA),
   ALT_FREQ = as.numeric(NA),
   GB_FEATURE = as.character(NA),
-  synonimous = as.character(NA),
+  SYNONYMOUS = as.character(NA),
   POS = as.numeric(NA),
   ALT = as.character(NA),
   NV_class = as.character(NA),
@@ -58,7 +58,7 @@ vcf <- vcf %>%
     VARIANT_NAME,
     ALT_FREQ,
     GB_FEATURE,
-    synonimous,
+    SYNONYMOUS,
     POS,
     ALT
   )
@@ -94,7 +94,7 @@ vcf <- vcf %>%
     ),
     Class = case_when(
       GB_FEATURE == "Intergenic" ~ "Intergenic",
-      TRUE ~ synonimous
+      TRUE ~ SYNONYMOUS
     ),
     POS = as.numeric(POS)
   ) %>%

workflow/scripts/report/evo_plots.R

@@ -26,7 +26,7 @@ vcf <- vcf %>%
     REGION,
     ALT_FREQ,
     GB_FEATURE,
-    synonimous,
+    SYNONYMOUS,
     POS
   )
 
@@ -45,12 +45,12 @@ vcf <- left_join(vcf, metadata)
 # PLOT
 log_info("Ploting dN and dS over time")
 plot_df <- vcf %>%
-  group_by(SAMPLE, synonimous) %>%
+  group_by(SAMPLE, SYNONYMOUS) %>%
   summarise(
     Freq = sum(ALT_FREQ, na.rm = TRUE)
   ) %>%
   pivot_wider(
-    names_from = synonimous,
+    names_from = SYNONYMOUS,
     values_from = Freq,
     values_fill = 0
   ) %>%
@@ -135,12 +135,12 @@ ggsave(
 # PLOT TABLES
 log_info("Saving plot table")
 vcf %>%
-  group_by(SAMPLE, synonimous) %>%
+  group_by(SAMPLE, SYNONYMOUS) %>%
   summarise(
     Freq = sum(ALT_FREQ, na.rm = TRUE)
   ) %>%
   pivot_wider(
-    names_from = synonimous,
+    names_from = SYNONYMOUS,
     values_from = Freq,
     values_fill = 0
   ) %>%