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Utilities/for_fastas/Plotcomps_speciesName.R

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+#load necessary packages
+library(tidyverse)
+
+#Change to the path of the directory you're working from
+#Use "getwd()" in console below to get path
+#You may need to change name of data frame below
+#if you used the CUB_v2.1.py script from Github, it should be in the 
+#CUBOutput folder and then inside the SpreadSheets folder
+#you are looking for the CompTrans.ENc.Raw.tsv
+gc3 <- data.frame(read_tsv('ENc.Raw.tsv'))|>
+  mutate(taxon = paste(substr(SequenceID, 1, 5), substr(SequenceID,6,10), sep = '')) #this line reads in your 10-digit codes to a column in the data frame called taxon
+
+spp <- data.frame(read_tsv('Species_name.tsv'))
+# Set the maximum text length you want
+
+spp$Species <- sapply(strsplit(spp$Species, " "), function(words) {
+  if (sum(nchar(words)) > 20) {
+    words[2] <- "spp"  
+  }
+  paste(words, collapse = " ")
+})
+gc3$taxon_a <- gc3$taxon
+for (i in seq_len(nrow(spp))) {
+  gc3$taxon_a <- gsub(spp$ten_digit_code[i], spp$Species[i], gc3$taxon_a)
+}
+
+gc3 <- gc3 %>%
+  group_by(taxon) %>%
+  mutate(taxon_c = paste0(taxon_a, '\n', taxon,', ',n()))
+
+#This .tsv is generated by the CUB script and will be in the same folder as the .tsv above
+#This generates the null expectation line
+enc_null <- data.frame(read_tsv('ENc.Null.tsv'))
+
+#change data in first line here to what you want plotted
+#you need as.numeric to ensure R is reading the variable correctly
+gc3_plot <- ggplot(gc3, aes(as.numeric(GC3.Degen), as.numeric(ObsWrightENc_No6Fold)))+
+  geom_point(size = 0.1)+
+  geom_line(data = enc_null, aes(GC3, ENc))+
+  theme_classic()+
+  labs(x = 'GC3 Degen', y = 'ObsWrightENc_No6fold')+
+  theme(legend.position = 'none', strip.text = element_text(size = 7))+
+  ggtitle("R2G NTD files")+
+  theme( axis.text.x=element_text(colour="black"))+
+  theme(axis.text.y=element_text(colour="black"))+
+  facet_wrap(~taxon_c)
+gc3_plot