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added logoP_logolas.R to plot logolas like plot to show ED regions

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Tanushree Tunstall 2022-01-24 17:23:32 +00:00
parent 9aa62b33b1
commit 6a9f4a0cab
4 changed files with 418 additions and 32 deletions
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41
scripts/functions/tests/test_logo_plots.R
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@ -1,5 +1,5 @@
#source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/config/pnca.R") # YES
source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/alr.R")
@ -72,37 +72,12 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# To plot entire MSA, simply don't specify {plot_positions}
# script: logoP_msa.R
# TODO perhaps: ED logo from Logolas
# TODO: Add scaled data option
########################################
# LogoPlotMSA(msaSeq_mut = msa_seq
# , msaSeq_wt = wt_seq
# , msa_method = 'bits' # or probability
# , my_logo_col = "taylor"
# , plot_positions = active_aa_pos
# , x_lab = "nsSNP position"
# , y_lab = ""
# , x_ats = 10 # text size
# , x_tangle = 90 # text angle
# , x_axis_offset = 0.05
# , y_ats = 15
# , y_tangle = 0
# , x_tts = 13 # title size
# , y_tts = 15
# , 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 = 16 # leg text size
# , leg_tts = 16 # leg title size
# )
########################################
# ED Logo plot MSA
# Mutant and wild-type
########################################
LogoPlotED(msaSeq_mut = msa_seq
LogoPlotMSA(msaSeq_mut = msa_seq
, msaSeq_wt = wt_seq
, msa_method = 'bits' # or probability
, my_logo_col = "taylor"
, my_logo_col = "taylor"
, plot_positions = active_aa_pos
, x_lab = "nsSNP position"
, y_lab = ""
@ -117,4 +92,10 @@ LogoPlotED(msaSeq_mut = msa_seq
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 16 # leg text size
, leg_tts = 16 # leg title size
)
)
########################################
# ED Logo plot MSA
# Mutant and wild-type
########################################