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Tanushree Tunstall 2022-08-17 18:42:15 +01:00
parent cd9b1ad245
commit c9d7ea9fad
10 changed files with 208 additions and 128 deletions
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2
config/alr.R
View file

@ -107,6 +107,6 @@ if ( all(c1, c2, c3) ) {
aa_pos_lig1 = NULL aa_pos_lig1 = NULL
aa_pos_lig2 = NULL aa_pos_lig2 = NULL
aa_pos_lig3 = NULL aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("ALR","DSL","CDL","Ca"), tile_map=data.frame(tile=c("ALR","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey","navyblue","purple"))

4
config/embb.R
View file

@ -104,7 +104,7 @@ cat("\n==================================================="
, aa_pos_ca , aa_pos_ca
, "\nNo. of ligand 'CDL' binding residues:" , length(aa_pos_cdl), "\n" , "\nNo. of ligand 'CDL' binding residues:" , length(aa_pos_cdl), "\n"
, aa_pos_cdl , aa_pos_cdl
, "\nNo. of ligand 'DSL' binding residues:" , length(aa_pos_dsl), "\n" , "\nNo. of ligand 'DPA' binding residues:" , length(aa_pos_dsl), "\n"
, aa_pos_dsl, "\n" , aa_pos_dsl, "\n"
) )
############################################################## ##############################################################
@ -117,6 +117,6 @@ aa_pos_lig1 = aa_pos_dsl #slategray
aa_pos_lig2 = aa_pos_cdl #navy blue aa_pos_lig2 = aa_pos_cdl #navy blue
aa_pos_lig3 = aa_pos_ca #purple aa_pos_lig3 = aa_pos_ca #purple
tile_map=data.frame(tile=c("EMB","DSL","CDL","Ca"), tile_map=data.frame(tile=c("EMB","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey","navyblue","purple"))

2
config/gid.R
View file

@ -132,6 +132,6 @@ cat("\n==================================================="
aa_pos_lig1 = aa_pos_rna aa_pos_lig1 = aa_pos_rna
aa_pos_lig2 = aa_pos_sam aa_pos_lig2 = aa_pos_sam
aa_pos_lig3 = aa_pos_amp aa_pos_lig3 = aa_pos_amp
tile_map=data.frame(tile=c("GID","DSL","CDL","Ca"), tile_map=data.frame(tile=c("GID","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey","navyblue","purple"))

2
config/katg.R
View file

@ -106,6 +106,6 @@ cat("\n==================================================="
aa_pos_lig1 = aa_pos_hem aa_pos_lig1 = aa_pos_hem
aa_pos_lig2 = NULL aa_pos_lig2 = NULL
aa_pos_lig3 = NULL aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("KAT","DSL","CDL","Ca"), tile_map=data.frame(tile=c("KAT","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey","navyblue","purple"))

2
config/pnca.R
View file

@ -56,6 +56,6 @@ aa_pos_lig2 = NULL
aa_pos_lig3 = NULL aa_pos_lig3 = NULL
#aa_pos_lig2 = aa_pos_catalytic #aa_pos_lig2 = aa_pos_catalytic
#aa_pos_lig3 = aa_pos_hbond #aa_pos_lig3 = aa_pos_hbond
tile_map=data.frame(tile=c("PZA","DSL","CDL","Ca"), tile_map=data.frame(tile=c("PZA","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey","navyblue","purple"))

2
config/rpob.R
View file

@ -59,6 +59,6 @@ cat("\n==================================================="
aa_pos_lig1 = NULL aa_pos_lig1 = NULL
aa_pos_lig2 = NULL aa_pos_lig2 = NULL
aa_pos_lig3 = NULL aa_pos_lig3 = NULL
tile_map=data.frame(tile=c("RPO","DSL","CDL","Ca"), tile_map=data.frame(tile=c("RPO","DPA","CDL","Ca"),
tile_colour=c("green","darkslategrey","navyblue","purple")) tile_colour=c("green","darkslategrey","navyblue","purple"))

113
scripts/functions/bp_subcolours.R
View file

@ -36,10 +36,10 @@ ColourPalleteMulti = function(df, group, subgroup){
bp_stability_hmap <- function(plot_df = merged_df3 bp_stability_hmap <- function(plot_df = merged_df3
, xvar_colname = "position" , xvar_colname = "position"
, yvar_colname = 'duet_scaled' # Only here so that you can do function(df) , yvar_colname = 'avg_stability_scaled' # Only here so that you can do function(df)
#, bar_col_colname = "group" #, bar_col_colname = "group"
, stability_colname = "duet_scaled" # Only here so that you can do function(df) , stability_colname = "avg_stability_scaled" # Only here so that you can do function(df)
, stability_outcome_colname = "duet_outcome" # Only here so that you can do function(df) , stability_outcome_colname = "avg_stability_outcome" # Only here so that you can do function(df)
, p_title = "DUMMY TITLE", # Only here so that you can do function(df) , p_title = "DUMMY TITLE", # Only here so that you can do function(df)
my_xaxls = 6, # x-axis label size my_xaxls = 6, # x-axis label size
my_yaxls = 6, # y-axis label size my_yaxls = 6, # y-axis label size
@ -54,7 +54,10 @@ bp_stability_hmap <- function(plot_df = merged_df3
, lig_dist_colname = LigDist_colname # from globals , lig_dist_colname = LigDist_colname # from globals
, tpos0 = 0 # 0 is a magic number that does my sensible default , tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1 , tW0 = 1
, tH0 = 0.2 , tH0 = 0.2,
y_max_override = 1, # an override for tidily plotting multiple different-ranged plots together
reorder_position = FALSE # enable to reorder according to plot_df$pos_count
@ -62,7 +65,7 @@ bp_stability_hmap <- function(plot_df = merged_df3
{ {
# Custom 2: x-axis geom tiles ~ lig distance # Custom 2: x-axis geom tiles ~ lig distance
# order the df by position and ensure it is a factor # order the df by position and ensure it is a factor
plot_df = plot_df[order(plot_df[[xvar_colname]]), ] plot_df = plot_df[order(plot_df[[xvar_colname]]), ]
plot_df[[xvar_colname]] = factor(plot_df[[xvar_colname]]) plot_df[[xvar_colname]] = factor(plot_df[[xvar_colname]])
@ -76,10 +79,18 @@ bp_stability_hmap <- function(plot_df = merged_df3
# #
# Add col: 'group' # Add col: 'group'
plot_df$group = paste0(plot_df[[stability_outcome_colname]], "_", my_grp, sep = "") plot_df$group = paste0(plot_df[[stability_outcome_colname]], "_", my_grp, sep = "")
plot_df=plot_df %>% dplyr::add_count(position)
plot_df$pos_count=plot_df$n
plot_df$n=NULL
# check unique values in normalised data # define a "max Y" in case the user didn't supply one
# cat("\nNo. of unique values in", stability_colname, "no rounding:" if(reorder_position) {
# , length(unique(plot_df[[stability_colname]]))) y_max = max(plot_df$pos_count)
}
else{
y_max = 1 # boring default
}
y_axis_limit = round_any(y_max, y_max_override, ceiling)
# Call the function to create the palette based on the group defined above # Call the function to create the palette based on the group defined above
#subcols_ps #subcols_ps
@ -87,55 +98,63 @@ bp_stability_hmap <- function(plot_df = merged_df3
cat("\nNo. of sub colours generated:", length(subcols_bp_hmap)) cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
anno_bar=position_annotation(plot_df, anno_bar=position_annotation(plot_df,
aa_pos_drug=aa_pos_drug, reorder_position=reorder_position,
active_aa_pos=active_aa_pos, aa_pos_drug=aa_pos_drug,
aa_pos_lig1=aa_pos_lig1, active_aa_pos=active_aa_pos,
aa_pos_lig2=aa_pos_lig2, aa_pos_lig1=aa_pos_lig1,
aa_pos_lig3=aa_pos_lig3 aa_pos_lig2=aa_pos_lig2,
aa_pos_lig3=aa_pos_lig3
) )
# Generate the subcols barplot subcols_plot = ggplot(plot_df) +
cowplot::plot_grid( scale_fill_manual( values = subcols_bp_hmap
ggplot(plot_df, aes_string(x = xvar_colname , guide = "none") +
#, ordered = T # scale_x_discrete("Position", labels=factor(plot_df$position)) +
) scale_y_continuous(limits=c(0,y_axis_limit)) +
) + theme(
geom_bar(aes(fill = group) panel.grid = element_line(color="lightgrey", size=0.125)
, colour = "grey", size=0.125) + , axis.text.x = element_text(size = my_xaxls
scale_fill_manual( values = subcols_bp_hmap
, guide = "none") +
# scale_x_discrete("Position", labels=factor(plot_df$position)) +
theme(
panel.grid = element_line(color="lightgrey", size=0.125)
, axis.text.x = element_text(size = my_xaxls
, angle = 90 , angle = 90
, hjust = 1 , hjust = 1
, vjust = 0.4) , vjust = 0.4)
, axis.text.y = element_text(size = my_yaxls , axis.text.y = element_text(size = my_yaxls
, angle = 0 , angle = 0
, hjust = 1 , hjust = 1
, vjust = 0) , vjust = 0)
, axis.title.x = element_blank() , axis.title.x = element_blank()
, axis.ticks = element_blank() , axis.ticks = element_blank()
#, axis.title.x = element_text(size = my_xaxts) #, axis.title.x = element_text(size = my_xaxts)
, axis.title.y = element_text(size = my_yaxts ) , axis.title.y = element_text(size = my_yaxts )
, plot.title = element_text(size = my_pts , plot.title = element_text(size = my_pts
, hjust = 0.5) , hjust = 0.5)
# , panel.grid = element_blank() # , panel.grid = element_blank()
, panel.background = element_rect(fill = "transparent", colour=NA) , panel.background = element_rect(fill = "transparent", colour=NA)
) + ) +
labs(title = p_title labs(title = p_title
, x = my_xlab , x = my_xlab
, y = my_ylab), , y = my_ylab) +
if(reorder_position) {
geom_bar(aes(x=reorder(position,-pos_count), fill = group),
colour = "grey",
size=0.125
)
}else{
geom_bar(aes(x=position, fill = group),
colour = "grey",
size=0.125
)
}
# Generate the subcols barplot
cowplot::plot_grid(
subcols_plot,
NULL, NULL,
anno_bar, anno_bar,
#generate_distance_legend(plot_df),
ncol = 1, ncol = 1,
align = "v", align = "v",
rel_heights = c(6,-0.1,1) rel_heights = c(6,-0.1,1)
#rel_widths = c(9/10, 0.4/10)
) )
} }

44
scripts/functions/logoP_or.R
View file

@ -81,13 +81,11 @@ LogoPlotCustomH <- function(plot_df
if (rm_empty_y){ if (rm_empty_y){
cat(paste0("Original Rows: ",nrow(plot_df)))
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),] plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
cat("\nRemoving empty positions...\n") cat(paste0("Plotting Rows after removing NAs: ",nrow(plot_df)))
} }
y_max = max(plot_df[[y_axis_colname]], na.rm = T)
cat("\nRemoving y scale incremenet:", y_axis_increment)
y_lim = round_any(y_max, y_axis_increment, f = ceiling)
#------------------- #-------------------
# logo data: LogOR # logo data: LogOR
@ -98,8 +96,10 @@ LogoPlotCustomH <- function(plot_df
plot_df[log_colname] = log_value(plot_df[y_axis_colname]) plot_df[log_colname] = log_value(plot_df[y_axis_colname])
logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)] logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, log_colname)] logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, log_colname, fill = 0.0)) logo_df_plot = logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)
rownames(logo_df_plot) = logo_df_plot$mutant_type
logo_df_plot$mutant_type = NULL
logo_dfP_wf=as.matrix(logo_df_plot)
#!!! For consideration: to add y_axis 'breaks' and 'limits' !!! #!!! For consideration: to add y_axis 'breaks' and 'limits' !!!
#y_max = max(plot_df[[log_colname]], na.rm = T) #y_max = max(plot_df[[log_colname]], na.rm = T)
#y_axis_increment = #y_axis_increment =
@ -114,18 +114,28 @@ LogoPlotCustomH <- function(plot_df
#------------------- #-------------------
logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)] logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)] logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)) logo_df_plot = logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0)
rownames(logo_df_plot) = logo_df_plot$mutant_type
logo_df_plot$mutant_type = NULL
logo_dfP_wf=as.matrix(logo_df_plot)
#logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
} }
#class(logo_dfP_wf) #class(logo_dfP_wf)
rownames(logo_dfP_wf) = logo_dfP_wf[,1] #rownames(logo_dfP_wf) = logo_dfP_wf[,1]
#dim(logo_dfP_wf) #dim(logo_dfP_wf)
logo_dfP_wf = logo_dfP_wf[,-1] #logo_dfP_wf = logo_dfP_wf[,-1]
#str(logo_dfP_wf) #str(logo_dfP_wf)
#y_max = max(plot_df[[y_axis_colname]], na.rm = T)
y_max = max(colSums(logo_dfP_wf))
cat("\nRemoving y scale incremenet:", y_axis_increment)
y_lim = round_any(y_max, y_axis_increment, f = ceiling)
#colnames(logo_dfP_wf) #colnames(logo_dfP_wf)
position_or = as.numeric(colnames(logo_dfP_wf)) position_or = as.numeric(colnames(logo_dfP_wf))
@ -167,11 +177,12 @@ LogoPlotCustomH <- function(plot_df
ggplot() + ggplot() +
geom_logo(logo_dfP_wf geom_logo(logo_dfP_wf
, method = "custom" , method = "custom"
#, method = "bits"
, col_scheme = my_logo_col , col_scheme = my_logo_col
, seq_type = "aa") + , seq_type = "aa") +
#ylab("my custom height") + #ylab("my custom height") +
theme( axis.ticks.x = element_blank() theme( axis.ticks = element_blank()
, axis.ticks.length = unit(0, "pt") #, axis.ticks.length = unit(0, "pt")
, axis.title.x = element_blank() , axis.title.x = element_blank()
# , axis.text.x = element_blank() # turn this off and the below on if you want to visually # , axis.text.x = element_blank() # turn this off and the below on if you want to visually
# verify positions. # verify positions.
@ -206,10 +217,13 @@ LogoPlotCustomH <- function(plot_df
, labels = position_or , labels = position_or
, limits = factor(1:length(position_or))) + , limits = factor(1:length(position_or))) +
scale_y_continuous(y_lab scale_y_continuous(y_lab,
, breaks = seq(0, (y_lim), by = y_axis_increment) breaks = seq(0,
#, labels = seq(0, (y_lim), by = y_axis_increment) (y_lim),
, limits = c(0, y_lim)) + by = y_axis_increment
),
limits = c(0, y_lim)
) +
labs(y=y_lab), labs(y=y_lab),
position_annotation(plot_df, position_annotation(plot_df,
bg = theme_bgc, bg = theme_bgc,

148
scripts/functions/position_annotation.R
View file

@ -3,6 +3,7 @@
# This plots position tiles for the (up to) three ligands as well as drug # This plots position tiles for the (up to) three ligands as well as drug
position_annotation=function(plot_df, position_annotation=function(plot_df,
bg="transparent", bg="transparent",
reorder_position = FALSE, # enable to reorder according to plot_df$pos_count
aa_pos_drug=1:100, aa_pos_drug=1:100,
active_aa_pos=1:100, active_aa_pos=1:100,
aa_pos_lig1=1:100, aa_pos_lig1=1:100,
@ -47,65 +48,112 @@ position_annotation=function(plot_df,
plot_df$col_bg3 = ifelse(plot_df[["position"]]%in%aa_pos_lig3 plot_df$col_bg3 = ifelse(plot_df[["position"]]%in%aa_pos_lig3
, "purple", plot_df$col_bg3) , "purple", plot_df$col_bg3)
# the call to generate_distance_colour_map should probably be
# wherever the outer DF is built, and not here.
plot_df = generate_distance_colour_map(plot_df, debug=TRUE) plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
heat_bar = ggplot(plot_df, heat_bar = ggplot(plot_df) + # THIS STUPID FUCKING FACTOR THING
aes(x=factor(position)) # THIS STUPID FUCKING FACTOR THING
) +
geom_tile(aes(y=0),
fill=plot_df$ligD_colours) +
# scale_x_discrete("Position", labels=factor(plot_df$position)) + # scale_x_discrete("Position", labels=factor(plot_df$position)) +
theme_nothing() + theme_nothing() +
theme(#axis.text.x = element_text(angle = 90, size = 6), theme(#axis.text.x = element_text(angle = 90, size = 6),
title = element_blank() title = element_blank()
) + # enable for alignment debug ) + # enable for alignment debug
labs(x = NULL, y = NULL) #end of distance-heat-bar labs(x = NULL, y = NULL) +
# if reorder_position is turned on then we need to reorder 'x'
# according to the pos_count column (creating this column is
# left as a fun exercise to whoever reads this next)
if(reorder_position) {
geom_tile(aes(y=0, x=reorder(position,-pos_count)),
fill=plot_df$ligD_colours)
} else {
geom_tile(aes(y=0, x=factor(position)),
fill=plot_df$ligD_colours)
}
#end of distance-heat-bar
#NULL, #NULL,
pos_tiles = ggplot(plot_df, if(reorder_position) {
aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING pos_tiles = ggplot(plot_df) +
) #scale_x_discrete("Position", labels=factor(plot_df$position)) +
) + scale_color_manual(values = c(
# geom_tile(aes(y = 0, fill = col_aa, colour = col_aa) "brown"="brown",
# ) + "green"="#00ff00",
geom_tile(aes(y = 1, fill = bg_all, colour = bg_all) "transparent"="transparent",
) + "slategrey"="#2f4f4f",
geom_tile(aes(y = 2, fill = col_bg1, colour = col_bg1) "navyblue"="#000080",
) + "purple"="#a020f0"
geom_tile(aes(y = 3, fill = col_bg2, colour = col_bg2) ),
) + #expand=c(0,0)
geom_tile(aes(y = 4, fill = col_bg3, colour = col_bg3) ) +
) + scale_fill_manual(values = c(
"brown"="brown",
"green"="#00ff00",
"transparent"="transparent",
"slategrey"="#2f4f4f",
"navyblue"="#000080",
"purple"="#a020f0"
),
#expand=c(0,0)
) +
theme_nothing() +
theme(plot.background = element_rect(fill = bg, colour=NA),
#plot.margin = margin(t=0,b=0),
panel.background = element_rect(fill = bg, colour=NA),
legend.position = "none"
) +
labs(x = NULL, y= NULL) +
geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all)
) +
geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
) +
geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
) +
geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
)
#scale_x_discrete("Position", labels=factor(plot_df$position)) + } else {
scale_color_manual(values = c( pos_tiles = ggplot(plot_df) +
"brown"="brown", #scale_x_discrete("Position", labels=factor(plot_df$position)) +
"green"="#00ff00", scale_color_manual(values = c(
"transparent"="transparent", "brown"="brown",
"slategrey"="#2f4f4f", "green"="#00ff00",
"navyblue"="#000080", "transparent"="transparent",
"purple"="#a020f0" "slategrey"="#2f4f4f",
), "navyblue"="#000080",
#expand=c(0,0) "purple"="#a020f0"
) + ),
scale_fill_manual(values = c( #expand=c(0,0)
"brown"="brown", ) +
"green"="#00ff00", scale_fill_manual(values = c(
"transparent"="transparent", "brown"="brown",
"slategrey"="#2f4f4f", "green"="#00ff00",
"navyblue"="#000080", "transparent"="transparent",
"purple"="#a020f0" "slategrey"="#2f4f4f",
), "navyblue"="#000080",
#expand=c(0,0) "purple"="#a020f0"
) + ),
theme_nothing() + #expand=c(0,0)
theme(plot.background = element_rect(fill = bg, colour=NA), ) +
#plot.margin = margin(t=0,b=0), theme_nothing() +
panel.background = element_rect(fill = bg, colour=NA), theme(plot.background = element_rect(fill = bg, colour=NA),
legend.position = "none" #plot.margin = margin(t=0,b=0),
) + panel.background = element_rect(fill = bg, colour=NA),
labs(x = NULL, y= NULL) legend.position = "none"
) +
labs(x = NULL, y= NULL) +
geom_tile(aes(y = 1, x=factor(position), fill = bg_all, colour = bg_all)
) +
geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)
) +
geom_tile(aes(y = 3, x=factor(position), fill = col_bg2, colour = col_bg2)
) +
geom_tile(aes(y = 4, x=factor(position), fill = col_bg3, colour = col_bg3)
)
}
# tile thingies end
heat_legend=get_legend(heat_bar) heat_legend=get_legend(heat_bar)
out_plot=cowplot::plot_grid( out_plot=cowplot::plot_grid(
heat_bar, heat_bar,
NULL, NULL,

11
scripts/plotting/plotting_thesis/gg_pairs_all.R
View file

@ -14,9 +14,8 @@ my_gg_pairs=function(plot_df, plot_title
title="ρ", title="ρ",
digits=2, digits=2,
justify_labels = "centre", justify_labels = "centre",
#title_args=c(colour="black"), title_args=list(size=tt_args_size, colour="black"),#2.5
title_args=c(size=tt_args_size),#2.5 group_args=list(size=gp_args_size)#2.5
group_args=c(size=gp_args_size)#2.5
) )
), ),
lower = list( lower = list(
@ -93,7 +92,7 @@ corr_ps_colnames = c(static_cols
corr_df_ps = corr_plotdf[, corr_ps_colnames] corr_df_ps = corr_plotdf[, corr_ps_colnames]
# Plot #1 # Plot #1
plot_corr_df_ps = my_gg_pairs(corr_df_ps, plot_title="Stability features") plot_corr_df_ps = my_gg_pairs(corr_df_ps, plot_title="Stability estimates")
########################################################## ##########################################################
#================ #================
# Conservation # Conservation
@ -109,7 +108,7 @@ corr_conservation_cols = c( static_cols
corr_df_cons = corr_plotdf[, corr_conservation_cols] corr_df_cons = corr_plotdf[, corr_conservation_cols]
# Plot #2 # Plot #2
plot_corr_df_cons = my_gg_pairs(corr_df_cons, plot_title="Conservation features") plot_corr_df_cons = my_gg_pairs(corr_df_cons, plot_title="Conservation estimates")
########################################################## ##########################################################
#================ #================
@ -139,7 +138,7 @@ corr_df_aff = corr_affinity_df[, corr_aff_colnames]
colnames(corr_df_aff) colnames(corr_df_aff)
# Plot #3 # Plot #3
plot_corr_df_aff = my_gg_pairs(corr_df_aff, plot_title="Affinity features", tt_args_size = 4, gp_args_size =4) plot_corr_df_aff = my_gg_pairs(corr_df_aff, plot_title="Affinity estimates", tt_args_size = 4, gp_args_size =4)
#============= #=============
# combine # combine