152 lines
5.8 KiB
R
152 lines
5.8 KiB
R
#source("~/git/LSHTM_analysis/config/gid.R")
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source("~/git/LSHTM_analysis/config/pnca.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/alr.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 = T
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# , log_value = log10
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# , y_axis_increment = 100
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# , rm_empty_y = T
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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 = 10 # 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(1)# can be 0,1, 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 = "nsSNP count"
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# , x_ats = 10 # text size
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# , x_tangle = 90 # text angle
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# , y_ats = 18
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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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# Can select active site residues
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# specify {plot_positions}
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# To plot entire MSA, simply don't specify {plot_positions}
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# script: logoP_msa.R
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########################################
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# LogoPlotMSA(msaSeq_mut = msa_seq
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# , msaSeq_wt = wt_seq
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# # , use_pfm
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# # , use_pfm_scaled
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# # , use_ed
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# , msa_method = 'bits' # or probability
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# , my_logo_col = "taylor"
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# , plot_positions = 1:15
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# , x_lab = "nsSNP position"
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# , y_lab = ""
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# , x_ats = 10 # text size
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# , x_tangle = 90 # text angle
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# , x_axis_offset = 0.05
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# , y_ats = 15
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# , y_tangle = 0
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# , x_tts = 13 # title size
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# , y_tts = 15
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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 = 16 # 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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# ED Logo plot MSA
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# Mutant and wild-type
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########################################
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# library(Logolas)
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# library(ggseqlogo)
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# source("~/git/LSHTM_analysis/scripts/functions/my_logolas.R")
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# source("~/git/LSHTM_analysis/scripts/functions/logoP_logolas.R")
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#
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# # data msa: mut
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# my_data = read.csv("/home/tanu/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
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# msaSeq_mut = my_data$V1
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# msa_seq = msaSeq_mut
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#
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# # data msa: wt
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# gene = "pncA"
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# drug = "pyrazinamide"
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# indir = paste0("~/git/Data/", drug , "/input/")
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#
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# in_filename_fasta = paste0(tolower(gene), "2_f2.fasta")
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# infile_fasta = paste0(indir, in_filename_fasta)
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# cat("\nInput fasta file for WT: ", infile_fasta, "\n")
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#
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# msa2 = read.csv(infile_fasta, header = F)
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# head(msa2)
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# cat("\nLength of WT fasta:", nrow(msa2))
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# wt_seq = msa2$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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#PlotLogolasMSA()
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PlotLogolasMSA(msaSeq_mut = msa_seq
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, msaSeq_wt = wt_seq
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, logo_type = c("bits_pfm") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw") # can be "bits", "probability" or "custom"
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, EDScore_type = c("log") # see if this relevant, or source function should have it!
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, bg_prob = NULL
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, my_logo_col = "taylor"
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, plot_positions = c(1:15)
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#, y_breaks
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, x_lab_mut = "nsSNP-position"
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#, y_lab_mut
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, x_ats = 13 # text size
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, x_tangle = 90 # text angle
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, x_axis_offset = 0.05
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, x_axis_offset_filtered = 0.05
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, y_axis_offset = 0.05
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, y_ats = 13
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, y_tangle = 0
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, x_tts = 13
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, y_tts = 13
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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 = 16 # leg text size
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, leg_tts = 16 # leg title size
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)
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