From 23bb087ea39ee73fc18b663830c7773f49e9d247 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 6 Sep 2022 17:06:01 +0100
Subject: [PATCH] plot function fixes for position tiles

---
 scripts/functions/logoP_or.R       |  5 -----
 scripts/functions/logoP_snp.R      | 13 +++++++------
 scripts/functions/wideP_consurf3.R |  9 +++------
 3 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/scripts/functions/logoP_or.R b/scripts/functions/logoP_or.R
index 0caee96..f86bb2d 100644
--- a/scripts/functions/logoP_or.R
+++ b/scripts/functions/logoP_or.R
@@ -215,11 +215,6 @@ LogoPlotCustomH <- function(plot_df
       labs(y=y_lab), 
     position_annotation(plot_df,
                         bg = theme_bgc,
-                        aa_pos_drug=aa_pos_drug,
-                        active_aa_pos=active_aa_pos,
-                        aa_pos_lig1=aa_pos_lig1,
-                        aa_pos_lig2=aa_pos_lig2,
-                        aa_pos_lig3=aa_pos_lig3,
                         ...
     ),
     
diff --git a/scripts/functions/logoP_snp.R b/scripts/functions/logoP_snp.R
index 0522141..9be50d6 100644
--- a/scripts/functions/logoP_snp.R
+++ b/scripts/functions/logoP_snp.R
@@ -283,12 +283,13 @@ LogoPlotSnps <- function(plot_df
   
   anno_bar = position_annotation(plot_df,
                                  bg = theme_bgc,
-                                 aa_pos_drug=aa_pos_drug,
-                                 active_aa_pos=active_aa_pos,
-                                 aa_pos_lig1=aa_pos_lig1,
-                                 aa_pos_lig2=aa_pos_lig2,
-                                 aa_pos_lig3=aa_pos_lig3,
-                                 ...)
+                                 # active_aa_pos = active_aa_pos,
+                                 # aa_pos_drug = aa_pos_drug,
+                                 # aa_pos_lig1 = aa_pos_lig1,
+                                 # aa_pos_lig2 = aa_pos_lig2,
+                                 # aa_pos_lig3 = aa_pos_lig3,
+                                 ...
+                                 )
   
   #aligned=align_plots(logo_top, logo_bottom, anno_bar, align='vh', axis='lr')
   cowplot::plot_grid(
diff --git a/scripts/functions/wideP_consurf3.R b/scripts/functions/wideP_consurf3.R
index 99eda2a..e4679a0 100644
--- a/scripts/functions/wideP_consurf3.R
+++ b/scripts/functions/wideP_consurf3.R
@@ -69,16 +69,13 @@ wideP_consurf3 <- function(plot_df
                            , default_gt_clr = "white"
                            , build_plot_df=FALSE
                            , debug=FALSE
+                           , ...
 ){
   anno_bar = position_annotation(
     plot_df,
     bg = panel_col,
-    aa_pos_drug=aa_pos_drug,
-    active_aa_pos=active_aa_pos,
-    aa_pos_lig1=aa_pos_lig1,
-    aa_pos_lig2=aa_pos_lig2,
-    aa_pos_lig3=aa_pos_lig3
-  )
+    ...
+    )
   
   if(missing(point_colours)){
     temp_cols = colorRampPalette(c("seagreen", "sienna3"))(30)