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This commit is contained in:
Tanushree Tunstall 2022-01-26 11:34:59 +00:00
parent 1c1e98ad4f
commit b133b8be24
4 changed files with 5 additions and 20 deletions
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13
scripts/functions/logoP.R
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@ -4,7 +4,6 @@
# one with OR # one with OR
# --> select/drop down option to remove empty positions # --> select/drop down option to remove empty positions
# --> easy peasy, just select the merged_df3_comp
# --> select/drop down option for colour # --> select/drop down option for colour
# --> if clustalx and taylor, set variable to black bg + white font # --> if clustalx and taylor, set variable to black bg + white font
# --> if chemistry and hydrophobicity, then grey bg + black font # --> if chemistry and hydrophobicity, then grey bg + black font
@ -17,13 +16,6 @@
# --> select/drop down option for colour # --> select/drop down option for colour
# --> should include WT # --> should include WT
# Data used
#wide_df_or # or logo plot
#wide_df_or_mult # > 1 sites
#wide_df_logor_m #make it as a scale option. REDUNDANT
#tab_mt # mutant logo plot
#tab_wt # wt logo plot
# Make it hover over position and then get the corresponding data table! # Make it hover over position and then get the corresponding data table!
#%%====================================================================== #%%======================================================================
@ -40,9 +32,6 @@
#, xtt_col = #, xtt_col =
#, ytt_col = #, ytt_col =
# ADD legend for hydrophobicity: done
# ADD option to remove empty positions
LogoPlotCustomH <- function(plot_df LogoPlotCustomH <- function(plot_df
, x_axis_colname = "position" , x_axis_colname = "position"
, y_axis_colname = "or_mychisq" , y_axis_colname = "or_mychisq"
@ -198,4 +187,4 @@ LogoPlotCustomH <- function(plot_df
return(LogoPlot) return(LogoPlot)
} }

4
scripts/functions/logoP_msa.R
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@ -1,7 +1,5 @@
source("~/git/LSHTM_analysis/scripts/plotting/Header_TT.R")
source("~/git/LSHTM_analysis/scripts/functions/ed_pfm_data.R")
########################################### ###########################################
PlotLogolasMSA <- function(msaSeq_mut # chr vector LogoPlotMSA <- function(msaSeq_mut # chr vector
, msaSeq_wt # chr vector , msaSeq_wt # chr vector
#, msa_method = c("custom") # can be "bits", "probability" or "custom" #, msa_method = c("custom") # can be "bits", "probability" or "custom"
, logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw") # can be "bits", "probability" or "custom" , logo_type = c("EDLogo") #"bits_pfm", "probability_pfm", "bits_raw", "probability_raw") # can be "bits", "probability" or "custom"

5
scripts/functions/tests/test_logo_plots.R
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@ -1,11 +1,11 @@
#source("~/git/LSHTM_analysis/config/gid.R") #source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/pnca.R") source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/embb.R") #source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/alr.R") #source("~/git/LSHTM_analysis/config/alr.R")
#source("~/git/LSHTM_analysis/config/rpob.R") #source("~/git/LSHTM_analysis/config/rpob.R")
#--------------------------------------------------- #---------------------------------------------------
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
################################ ################################
# Logo plot with custom Y axis # Logo plot with custom Y axis
@ -70,7 +70,6 @@
# specify {plot_positions} # specify {plot_positions}
# To plot entire MSA, simply don't specify {plot_positions} # To plot entire MSA, simply don't specify {plot_positions}
# script: logoP_msa.R # script: logoP_msa.R
# TODO: Add scaled data option
######################################## ########################################
# LogoPlotMSA(msaSeq_mut = msa_seq # LogoPlotMSA(msaSeq_mut = msa_seq
# , msaSeq_wt = wt_seq # , msaSeq_wt = wt_seq

3
scripts/plotting/Header_TT.R
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@ -173,10 +173,9 @@ if(!require(protr)){
# install.packages("BiocManager") # install.packages("BiocManager")
#BiocManager::install("Logolas") #BiocManager::install("Logolas")
library("Logolas") #library("Logolas")
library("Biostrings") library("Biostrings")
#################################### ####################################
# Load all my functions: # Load all my functions:
# only works if tidyverse is loaded # only works if tidyverse is loaded