diff --git a/scripts/functions/logoP.R b/scripts/functions/logoP.R
index 3066d9c..96bd0a5 100644
--- a/scripts/functions/logoP.R
+++ b/scripts/functions/logoP.R
@@ -4,7 +4,6 @@
 
 # one with OR
   # --> select/drop down option to remove empty positions
-      # --> easy peasy, just select the merged_df3_comp
   # --> select/drop down option for colour
       # --> if clustalx and taylor,  set variable to black bg + white font
       # --> if chemistry and hydrophobicity, then grey bg +  black font 
@@ -17,13 +16,6 @@
   # --> select/drop down  option for colour
   # --> 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!
 #%%======================================================================
 
@@ -40,9 +32,6 @@
     #, xtt_col = 
     #, ytt_col = 
 
-# ADD legend for hydrophobicity: done
-# ADD option to remove empty positions
-
 LogoPlotCustomH <- function(plot_df
                      , x_axis_colname = "position"
                      , y_axis_colname = "or_mychisq"
@@ -198,4 +187,4 @@ LogoPlotCustomH <- function(plot_df
 
   return(LogoPlot)
 
-}
\ No newline at end of file
+}
diff --git a/scripts/functions/logoP_msa.R b/scripts/functions/logoP_msa.R
index 637098e..db97a5c 100644
--- a/scripts/functions/logoP_msa.R
+++ b/scripts/functions/logoP_msa.R
@@ -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
                         #, 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"
diff --git a/scripts/functions/tests/test_logo_plots.R b/scripts/functions/tests/test_logo_plots.R
index c61b1cb..8b90551 100644
--- a/scripts/functions/tests/test_logo_plots.R
+++ b/scripts/functions/tests/test_logo_plots.R
@@ -1,11 +1,11 @@
 #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/katg.R")
 #source("~/git/LSHTM_analysis/config/alr.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
@@ -70,7 +70,6 @@
   # specify {plot_positions}
   # To plot entire MSA, simply don't specify {plot_positions}
 # script: logoP_msa.R
-# TODO: Add scaled data option
 ########################################
 # LogoPlotMSA(msaSeq_mut = msa_seq
 #             , msaSeq_wt = wt_seq
diff --git a/scripts/plotting/Header_TT.R b/scripts/plotting/Header_TT.R
index 54336b7..c0d43e3 100755
--- a/scripts/plotting/Header_TT.R
+++ b/scripts/plotting/Header_TT.R
@@ -173,10 +173,9 @@ if(!require(protr)){
 #  install.packages("BiocManager")
 
 #BiocManager::install("Logolas")
-library("Logolas")
+#library("Logolas")
 library("Biostrings")
 
-
 ####################################
 # Load all my functions:
 # only works if tidyverse is loaded