37 lines
981 B
R
37 lines
981 B
R
source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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source("~/git/LSHTM_analysis/scripts/functions/ed_pfm_data.R")
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# data msa: mut
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my_data = read.csv("~/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
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msaSeq_mut = my_data$V1
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msa_seq = msaSeq_mut
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# data msa: wt
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gene = "pncA"
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drug = "pyrazinamide"
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indir = paste0("~/git/Data/", drug , "/input/")
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in_filename_fasta = paste0(tolower(gene), "2_f2.fasta")
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infile_fasta = paste0(indir, in_filename_fasta)
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cat("\nInput fasta file for WT: ", infile_fasta, "\n")
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msa2 = read.csv(infile_fasta, header = F)
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head(msa2)
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cat("\nLength of WT fasta:", nrow(msa2))
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wt_seq = msa2$V1
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head(wt_seq)
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msaSeq_wt = msa2$V1
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wt_seq = msaSeq_wt
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################################
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# DataED_PFM():
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# script: ed_pfm_data.R
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################################
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data_ed = DataED_PFM(msa_seq, wt_seq)
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names(data_ed)
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#par(mfrow = c(2,1))
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#logomaker(msa_seq, type = "EDLogo")
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ggseqlogo(data_ed[['combED_mutM']]
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, method = "custom")
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