From 28d572502da02fcb1f8a04fc090ad4aeffadd54c Mon Sep 17 00:00:00 2001
From: katiesevans <kathrynevans2015@u.northwestern.edu>
Date: Mon, 7 Feb 2022 11:23:07 -0600
Subject: [PATCH] small changes divergent script

---
 README.md                                     |  2 +-
 ...zied_divergent_region_characterization.Rmd | 22 ++++++++++---------
 main.nf                                       |  2 +-
 3 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 3150b4a..37a2f5e 100644
--- a/README.md
+++ b/README.md
@@ -120,7 +120,7 @@ The `sample sheet` has the following columns:
 Path to the **folder** containing both the hard-filtered and soft-filtered vcf outputs from [`wi-gatk`](https://github.com/AndersenLab/wi-gatk). VCF should contain **ALL** strains, the first step will be to subset isotype reference strains for further analysis.
 
 !!! Note
-    This should be the **path to the folder**, we want to isotype-subset both hard and soft filtered VCFs. For example: `--vcf_folder /projects/b1059/projects/Katie/wi-gatk/WI-20210121/variation/`
+    This should be the **path to the folder**, we want to isotype-subset both hard and soft filtered VCFs. For example: `--vcf_folder /projects/b1059/projects/Katie/wi-gatk/WI-20210121/variation/` or `--vcf_folder /projects/b1059/data/c_elegans/WI/variation/20210121/vcf/`
 
 ### --species (optional)
 
diff --git a/bin/reoptimzied_divergent_region_characterization.Rmd b/bin/reoptimzied_divergent_region_characterization.Rmd
index b2a5b0b..6bbbc6a 100644
--- a/bin/reoptimzied_divergent_region_characterization.Rmd
+++ b/bin/reoptimzied_divergent_region_characterization.Rmd
@@ -19,6 +19,7 @@ library(tidyr)
 library(readr)
 library(stringr)
 library(purrr)
+library(ggplot2)
 #library(glue)
 
 #setwd(glue::glue("{dirname(rstudioapi::getActiveDocumentContext()$path)}/.."))
@@ -430,8 +431,9 @@ readr::write_tsv(df_div_all_clustered, "All_divergent_regions_clustered.tsv")
 df_chr_length <- data.table::fread("df_chr_length.tsv")
 
 # order by size of total divergent regions per strain
+colnames(div_bed) <- c("CHROM", "start", "stop", "strain")
+
 div_bed <- div_bed %>%
-  dplyr::rename(CHROM = V1, start = V2, stop = V3, strain = V4) %>%
   dplyr::mutate(size = stop - start) %>%
   dplyr::group_by(strain) %>%
   dplyr::mutate(total = sum(size)) %>%
@@ -440,11 +442,11 @@ div_bed$strain <- factor(div_bed$strain, levels = unique(div_bed$strain))
 
 div_bed %>%
   na.omit() %>%
-  ggplot(.) +
-  geom_rect(data=df_chr_length, aes(xmin =  start/1e6, xmax = stop/1e6), ymin = div_bed$strain[1], ymax=div_bed$strain[1], color='transparent', fill='transparent', size =0.1) +
-  geom_rect(aes(xmin =  start/1e6, xmax = stop/1e6, ymin = strain , ymax = strain), fill = 'black',color='black', size = 0.5) +
-  theme_bw(12) +
-  theme(#axis.text.x = element_text(face = "bold"), 
+  ggplot2::ggplot(.) +
+  ggplot2::geom_rect(data=df_chr_length, aes(xmin =  start/1e6, xmax = stop/1e6), ymin = div_bed$strain[1], ymax=div_bed$strain[1], color='transparent', fill='transparent', size =0.1) +
+  ggplot2::geom_rect(aes(xmin =  start/1e6, xmax = stop/1e6, ymin = strain , ymax = strain), fill = 'black',color='black', size = 0.5) +
+  ggplot2::theme_bw(12) +
+  ggplot2::theme(#axis.text.x = element_text(face = "bold"), 
         axis.text.y  = element_blank(), 
         legend.position = 'none',
         axis.title=element_text(face = "bold"),
@@ -453,10 +455,10 @@ div_bed %>%
         # panel.spacing = unit(0.1, "lines"), 
         panel.grid = element_blank()) +
   # scale_y_continuous(expand = c(0.00, 0.00), limits=c(0.4,327.6)) +
-  scale_x_continuous(expand = c(0.02, 0.02), breaks = c(5, 10, 15)) +
-  facet_grid(~CHROM, scales="free",space = 'free') +
-  labs(x="Genomic position (Mb)",y= glue::glue("{length(unique(div_bed$strain))} wild isotypes"))
-ggsave("divergent_regions.png", height = 5, width = 7.5)
+  ggplot2::scale_x_continuous(expand = c(0.02, 0.02), breaks = c(5, 10, 15)) +
+  ggplot2::facet_grid(~CHROM, scales="free",space = 'free') +
+  ggplot2::labs(x="Genomic position (Mb)",y= glue::glue("{length(unique(div_bed$strain))} wild isotypes"))
+ggplot2::ggsave("divergent_regions.png", height = 5, width = 7.5)
 
 
 ```
diff --git a/main.nf b/main.nf
index 814e892..44a8982 100644
--- a/main.nf
+++ b/main.nf
@@ -274,7 +274,7 @@ process subset_iso_ref_strains {
     fi
 
     # output list of strains for divergent
-    bcftools query -l ${vcf} > div_isotype_list.txt
+    bcftools query -l \${output} > div_isotype_list.txt
 
     """