file name changes

AndersenLab · Feb 10, 2022 · 19b1159 · 19b1159
1 parent 28d5725
commit 19b1159
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 6 deletions.
diff --git a/bin/process_ibd_nf_final.R b/bin/process_ibd_nf_final.R
@@ -303,8 +303,9 @@ ggplot(plot_df,
     facet_grid(.~chromosome, scales="free", space="free") +
     theme(legend.position="none")
 
-ggsave("haplotype.pdf", height = 48, width = 24)
-ggsave("haplotype3.pdf", height = 70, width = 35, limitsize = FALSE)
+# might need to make longer with more strains...
+ggsave("haplotype.pdf", height = 70, width = 35, limitsize = FALSE)
+ggsave("haplotype.png", height = 70, width = 35, limitsize = FALSE)
 
 
 
@@ -332,7 +333,7 @@ ggplot(plot_df,
     facet_grid(.~chromosome, scales="free", space="free") +
     theme(legend.position="none")
 
-ggsave(paste("max_haplotype_genome_wide.pdf"),
+ggsave(paste("sweep.pdf"),
        height = 70, width = 35, limitsize = FALSE)
 
 #===============#

diff --git a/bin/reoptimzied_divergent_region_characterization.Rmd b/bin/reoptimzied_divergent_region_characterization.Rmd
@@ -288,9 +288,13 @@ write.csv(df_divergent_final_isotype, file="DataS3_divergent_regions_isotypes.cs
 
 div_bed <- df_divergent_final_isotype %>% 
   dplyr::select(CHROM, cluster_start, cluster_end, STRAIN) %>% 
-  dplyr::arrange(CHROM, cluster_start) 
+  dplyr::arrange(CHROM, cluster_start) %>%
+  dplyr::mutate(cluster_start = as.numeric(cluster_start),
+                cluster_end = as.numeric(cluster_end))
 
-write.table(div_bed, "divergent_regions_strain.bed", quote=F, col.names = F, row.names=F, sep="\t")
+# write.table(div_bed, "divergent_regions_strain.bed", quote=F, col.names = F, row.names=F, sep="\t")
+# see if this avoids the errors with 1.4e+07...
+readr::write_tsv(div_bed, "divergent_regions_strain.bed", col_names = F)
 
 ## total size
 
@@ -374,6 +378,7 @@ df_div_all <- df_divergent_final %>%
   dplyr::arrange(., chr, start)
 
 readr::write_tsv(df_div_all, "All_divergent_regions.tsv")
+readr::write_tsv(df_div_all, "divergent_regions_all.bed")
 
 ## clustered
 

diff --git a/main.nf b/main.nf
@@ -550,7 +550,7 @@ process define_divergent_region {
         file("*")
 
     output:
-        tuple file("divergent_regions_strain.bed"), file("divergent_regions.png")
+        tuple file("divergent_regions_strain.bed.gz"), file("divergent_regions_all.bed.gz"), file("divergent_regions.png")
 
     """
     cp ${workflow.projectDir}/bin/reoptimzied_divergent_region_characterization.Rmd reoptimzied_divergent_region_characterization.Rmd
@@ -562,6 +562,11 @@ process define_divergent_region {
     cp ${params.bin_bed} ./divergent_bins.bed
     cp divergent_regions_strain.bed ./divergent_df_isotype.bed
 
+    # gzip divergent files
+    gzip divergent_regions_strain.bed
+    cp All_divergent_regions.tsv divergent_regions_all.bed
+    gzip divergent_regions_all.bed
+
     """
 }