113 lines
4.2 KiB
R
113 lines
4.2 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_or.R
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################################
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LP1<- 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 = 50
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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 = 10 # text size
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, x_tangle = 90 # text angle
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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 = 13
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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 SAVs 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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LP2<- 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 0,1, 2, etc.# DD
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, my_logo_col = "chemistry" #DD
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, x_lab = "Wild-type position"
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, y_lab = "SAV count"
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, x_ats = 10
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, x_tangle = 90
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, y_ats = 15
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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 = 14
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, leg_tts = 16
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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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# Logo type:
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# EDLogo
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# Bits/probability (PFM matrix)
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# Bits/probability (Raw MSA data)
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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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# to select a small dataset: see test_ed_pfm_data.R
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#####################################################
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LP3<- LogoPlotMSA(unified_msa
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#msaSeq_mut = msa_seq
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#, msaSeq_wt = wt_seq
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, logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
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, EDScore_type = c("log")
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, bg_prob = NULL
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, my_logo_col = "chemistry"
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#, plot_positions = c(5:10, 92, 195, 118:119)
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, x_axis_offset = 0.02
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, x_axis_offset_filtered = 0.05
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, y_axis_offset = 0.05
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#, y_breaks = c(0, 2, 4, 6, 8, 10, 12)
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, x_lab_mut = "SAV-position"
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#, y_lab_mut
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, x_ats = 10
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, x_tangle = 90
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, y_ats = 12
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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"
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, leg_dir = "horizontal"
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, leg_ts = 16
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, leg_tts = 16
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)
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out_logoP = cowplot::plot_grid(LP3, LP1, LP2
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, nrow = 3
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, ncol = 1
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, rel_width = c(1/3, 0.5/3, 1/3)
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, rel_heights = c(0.8/2, 0.5/2, 0.7/2)
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, align = "hv")
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out_logoP
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