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tried ED logo, but needs work

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Tanushree Tunstall 2022-01-18 16:53:16 +00:00
parent 00094f036a
commit 8f8a9db92c
3 changed files with 119 additions and 108 deletions
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133
scripts/functions/tests/test_logo_plots.R
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@ -7,83 +7,84 @@ source("~/git/LSHTM_analysis/config/gid.R")
# source("~/git/LSHTM_analysis/config/katg.R")
# source("~/git/LSHTM_analysis/config/rpob.R")
#---------------------------------------------------
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
################################
# Logo plot with custom Y axis
# mainly OR
# script: logoP.R
################################
LogoPlotCustomH (plot_df = merged_df3
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, y_axis_log = F
, log_value = log10
, y_axis_increment = 5
, rm_empty_y = F
, my_logo_col = 'chemistry'
, x_lab = "Wild-type position"
, y_lab = "Odds Ratio"
, x_ats = 12 # text size
, x_tangle = 90 # text angle
, y_ats = 22
, y_tangle = 0
, x_tts = 19 # title size
, y_tts = 22
#, leg_pos = c(0.05,-0.12)
, leg_pos = "top"
, leg_dir = "horizontal"
, leg_ts = 15 # leg text size
, leg_tts = 16 # leg title size
)
########################################
# Logo plot showing nsSNPs by positions
# wild-type and mutant aa
# script: logoP_snp.R
########################################
LogoPlotSnps(plot_df = merged_df3
, x_axis_colname = "position"
, symbol_mut_colname = "mutant_type"
, symbol_wt_colname = "wild_type"
, omit_snp_count = c(0)# can be 1, 2, etc.
, my_logo_col = "chemistry"
, x_lab = "Wild-type position"
, y_lab = ""
, x_ats = 13 # text size
, x_tangle = 90 # text angle
, y_ats = 20
, y_tangle = 0
, x_tts = 18 # title size
, y_tts = 18
, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" # can be vertical or horizontal
, leg_ts = 14 # leg text size
, leg_tts = 16 # leg title size
)
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#
# ################################
# # Logo plot with custom Y axis
# # mainly OR
# # script: logoP.R
# ################################
# LogoPlotCustomH (plot_df = merged_df3
# , x_axis_colname = "position"
# , y_axis_colname = "or_mychisq"
# , symbol_colname = "mutant_type"
# , y_axis_log = F
# , log_value = log10
# , y_axis_increment = 5
# , rm_empty_y = F
# , my_logo_col = 'chemistry'
# , x_lab = "Wild-type position"
# , y_lab = "Odds Ratio"
# , x_ats = 12 # text size
# , x_tangle = 90 # text angle
# , y_ats = 22
# , y_tangle = 0
# , x_tts = 19 # title size
# , y_tts = 22
# #, leg_pos = c(0.05,-0.12)
# , leg_pos = "top"
# , leg_dir = "horizontal"
# , leg_ts = 15 # leg text size
# , leg_tts = 16 # leg title size
# )
#
#
# # ########################################
# # # Logo plot showing nsSNPs by positions
# # # wild-type and mutant aa
# # # script: logoP_snp.R
# # ########################################
# LogoPlotSnps(plot_df = merged_df3
# , x_axis_colname = "position"
# , symbol_mut_colname = "mutant_type"
# , symbol_wt_colname = "wild_type"
# , omit_snp_count = c(0)# can be 1, 2, etc.
# , my_logo_col = "chemistry"
# , x_lab = "Wild-type position"
# , y_lab = ""
# , x_ats = 13 # text size
# , x_tangle = 90 # text angle
# , y_ats = 20
# , y_tangle = 0
# , x_tts = 18 # title size
# , y_tts = 18
# , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
# , leg_dir = "horizontal" # can be vertical or horizontal
# , leg_ts = 14 # leg text size
# , leg_tts = 16 # leg title size
# )
#
#
########################################
# Logo plot MSA
# Mutant and wild-type
# wild-type and mutant aa
# Can select active site residues
# specify {plot_positions}
# To plot entire MSA, simply don't specify {plot_positions}
# script: logoP_msa.R
########################################
# BOTH WORK
#LogoPlotMSA(msa_seq, wt_seq)
# TODO perhaps: ED logo from Logolas
########################################
LogoPlotMSA(msaSeq_mut = msa_seq
, msaSeq_wt = wt_seq
, msa_method = 'bits' # or probability
, my_logo_col = "chemistry"
, my_logo_col = "taylor"
#, plot_positions = active_aa_pos
, plot_positions
, x_lab = "Wild-type position"
, x_lab = "nsSNP position"
, y_lab = ""
, x_ats = 13 # text size
, x_ats = 10 # text size
, x_tangle = 90 # text angle
, y_ats = 13
, y_tangle = 0
@ -93,4 +94,4 @@ LogoPlotMSA(msaSeq_mut = msa_seq
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 16 # leg text size
, leg_tts = 16 # leg title size
)
)