From 3a2e7476e2eb79d97a217db7c7ad6feaa39a362a Mon Sep 17 00:00:00 2001
From: ElinorSterner <86856150+ElinorSterner@users.noreply.github.com>
Date: Mon, 3 Apr 2023 16:18:33 -0400
Subject: [PATCH] Add files via upload

---
 Utilities/For_Assemblies/plot_assemblies.R | 55 ++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 Utilities/For_Assemblies/plot_assemblies.R

diff --git a/Utilities/For_Assemblies/plot_assemblies.R b/Utilities/For_Assemblies/plot_assemblies.R
new file mode 100644
index 0000000..2691b8b
--- /dev/null
+++ b/Utilities/For_Assemblies/plot_assemblies.R
@@ -0,0 +1,55 @@
+library(ggplot2)
+library(tidyverse)
+library(scales)
+
+#read in data output by python script
+transcriptome_data <- read.csv('assembly_assessment.csv')
+
+#make a column combining ten digit code and taxon information
+transcriptome_data_expert_level <- transcriptome_data|>
+  mutate(taxon_id = paste(ten_digit_code, taxon_info, sep = "-"))
+
+#plot length vs coverage, faceted and labeled by taxon
+len_cov <- ggplot(transcriptome_data, aes(x = GC, y = length, color = taxon_info))+
+  geom_point(size = .5)+
+  ylim(200, 15000)+
+  facet_wrap(~ten_digit_code + taxon_info)+
+  ggtitle('GC% and length of Allogromia assembled transcripts')+
+  theme(strip.text = element_text(size = 7))
+
+ggsave('len_cov.png', device = 'png', width = 8.5, height = 6)#save plot
+
+
+#plot distribution of GC
+dist_gc <- ggplot(transcriptome_data_expert_level, aes(x = GC, fill = taxon_info))+
+  geom_histogram()+
+  facet_wrap(~factor(taxon_id, levels = unique(taxon_id)))+#  facet_grid(~factor(my_variable, levels=c('val1', 'val2', 'val3', ...)))
+  ggtitle('Distribution of GC')+
+  theme(strip.text = element_text(size = 5))
+dist_gc
+ggsave('gc_dist.png', device = 'png', width = 8, height = 6)
+
+
+#plot distribution of length
+dist_len <- ggplot(transcriptome_data_expert_level, aes(x = reorder(taxon_id,length), y = length, color = taxon_info, fill= taxon_info))+
+  geom_violin()+
+  geom_boxplot(color = 'Black', fill = 'NA', outlier.shape = NA, width = 0.5)+
+  ggtitle('Length Distribution')+
+  scale_y_continuous(labels = comma, trans = 'log10')+
+  ylab('Length (log10)')+
+  xlab('Ten digit code, taxon info')
+dist_len + theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
+
+ggsave('length_violin.png', device = 'png',width = 7.5, height = 6)
+
+
+#plot distribution of coverage
+dist_cov <- ggplot(transcriptome_data_expert_level, aes(x = reorder(taxon_id,cov), y = cov, color = taxon_info, fill= taxon_info))+
+  geom_violin()+
+  geom_boxplot(color = 'Black', fill = 'NA', outlier.shape = NA, width = 0.5)+
+  ggtitle('Distribution of coverage')+
+  scale_y_continuous(labels = comma, trans = 'log10')+
+  ylab('Coverage (log10)')+
+  xlab('Ten digit code, taxon info')
+dist_cov+theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))
+ggsave('cov_violin.png', device = 'png', width = 7.5, height = 6)