87 lines
3.1 KiB
R
87 lines
3.1 KiB
R
source("~/git/LSHTM_analysis/config/gid.R")
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#source("~/git/LSHTM_analysis/config/pnca.R") # YES
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#---------------------------------------------------
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# FIXME
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source("~/git/LSHTM_analysis/config/alr.R")
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source("~/git/LSHTM_analysis/config/embb.R")
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source("~/git/LSHTM_analysis/config/katg.R")
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source("~/git/LSHTM_analysis/config/rpob.R")
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#---------------------------------------------------
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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################################
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# Logo plot with custom Y axis
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# mainly OR
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# script: logoP.R
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################################
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LogoPlotCustomH (plot_df = merged_df3
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, x_axis_colname = "position"
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, y_axis_colname = "or_mychisq"
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, symbol_colname = "mutant_type"
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, y_axis_log = F
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, log_value = log10
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, y_axis_increment = 5
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, rm_empty_y = F
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, my_logo_col = 'chemistry'
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, x_lab = "Wild-type position"
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, y_lab = "Odds Ratio"
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, x_ats = 12 # text size
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, x_tangle = 90 # text angle
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, y_ats = 22
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, y_tangle = 0
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, x_tts = 19 # title size
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, y_tts = 22
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#, leg_pos = c(0.05,-0.12)
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, leg_pos = "top"
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, leg_dir = "horizontal"
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, leg_ts = 15 # leg text size
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, leg_tts = 16 # leg title size
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)
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########################################
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# Logo plot showing nsSNPs by positions
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# wild-type and mutant aa
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# script: logoP_snp.R
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########################################
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LogoPlotSnps(plot_df = merged_df3
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, x_axis_colname = "position"
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, symbol_mut_colname = "mutant_type"
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, symbol_wt_colname = "wild_type"
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, omit_snp_count = c(0)# can be 1, 2, etc.
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, my_logo_col = "chemistry"
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, x_lab = "Wild-type position"
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, y_lab = ""
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, x_ats = 13 # text size
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, x_tangle = 90 # text angle
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, y_ats = 20
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, y_tangle = 0
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, x_tts = 18 # title size
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, y_tts = 18
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, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
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, leg_dir = "horizontal" # can be vertical or horizontal
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, leg_ts = 14 # leg text size
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, leg_tts = 16 # leg title size
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)
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########################################
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# Logo plot MSA
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# Mutant and wild-type
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# wild-type and mutant aa
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# script: logoP_msa.R
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########################################
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# msa1 = read.csv("/home/tanu/git/Data/cycloserine/output/alr_msa.csv", header = F)
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# head(msa1)
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# msa_seq= msa1$V1
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# head(msa_seq)
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#
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# msa2 = read.csv("/home/tanu/git/Data/cycloserine/input/alr.1fasta", header = F)
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# head(msa2)
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# wt_seq = msa2$V1
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# head(wt_seq)
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#
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# # BOTH WORK
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# LogoPlotMSA(msa_seq, wt_seq)
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# LogoPlotMSA(msa1, msa2)
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