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