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39 lines
1.7 KiB
R
39 lines
1.7 KiB
R
'''
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#Author, date: Auden Cote-L'Heureux, last updated in September 2023 by Adri
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#Intent: To make a simple jellyfish plot from a dataset like the one produced by the CUB_v2.1.py script, also in the Github Utilities folder.
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#Input: CompTrans.ENc.Raw.tsv and ENc.Null.tsv
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#Output: Jellyfish plots
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'''
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#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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setwd("/Users/agrow/Desktop/NewCUB_meta/CUBOutput/SpreadSheets")
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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('CompTrans.ENc.Raw.tsv'))%>%
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mutate(taxon = paste(substr(SequenceID, 1, 4), 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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#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')+
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ggtitle("Metatranscriptomics 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(vars(taxon), scales = 'free_x')
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gc3_plot
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