Fixed bug in table processing for report

Author: gregdenay

scripts/write_report.Rmd

@@ -56,13 +56,13 @@ primers <- snakemake@params[["primers"]]
 
 * Run directory: `r workdir`
 
-* Number of sequences in database: `r scan(nsequences)`
+* Number of sequences in database: `r scan(nsequences, what = "character")`
 
-* Number of dereplicated sequences: `r scan(nderep)`
+* Number of dereplicated sequences: `r scan(nderep, what = "character")`
 
-* Number of taxids in database: `r scan(ntaxids)`
+* Number of taxids in database: `r scan(ntaxids, what = "character")`
 
-* Number of sequences filtered out because of too high N content: `r scan(nNfilt)`
+* Number of sequences filtered out because of too high N content: `r scan(nNfilt, what = "character")`
 
 * Primers were trimmed before alignment: `r trimming`
 
@@ -79,15 +79,15 @@ Pairwise comparison of sequences with less than `r identity*100`% identity was n
 
 ```{r distances}
 data_table <- read.csv(file = distanceTable, sep = '\t', check.names = FALSE)
-full_table <- data_table %>% rename (query = target, query_name = target_name, query_taxid = target_taxid,
-									target = query, target_name = query_name, target_taxid = query_taxid) %>%
-							bind_rows(data_table)
+inverted_table <- data_table %>% rename (query = target, query_name = target_name, query_taxid = target_taxid, query_relsize= target_relsize, query_size = target_size,
+									target = query, target_name = query_name, target_taxid = query_taxid, target_size = query_size, target_relsize = query_relsize) 
+full_table<- data_table %>% bind_rows(inverted_table)
 
 datatable(full_table, filter = list(position = 'top'), rownames = FALSE, escape = FALSE,
 		extensions= c("ColReorder", "Buttons"),
 		selection = 'none',
 		options = list(dom = 'BRrlftpi',
-						autoWidth=FALSE,
+						autoWidth=FALSE, 
 						scrollX = TRUE,
 						lengthMenu = list(c(50, 100, 500, -1), 
 										  c('50', '100', '500', 'All')),