AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
This commit is contained in:
parent
cd9b1ad245
commit
c9d7ea9fad
10 changed files with 208 additions and 128 deletions
|
|
@ -36,10 +36,10 @@ ColourPalleteMulti = function(df, group, subgroup){
|
|||
|
||||
bp_stability_hmap <- function(plot_df = merged_df3
|
||||
, 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"
|
||||
, stability_colname = "duet_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_colname = "avg_stability_scaled" # 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)
|
||||
my_xaxls = 6, # x-axis label size
|
||||
my_yaxls = 6, # y-axis label size
|
||||
|
|
@ -54,15 +54,18 @@ bp_stability_hmap <- function(plot_df = merged_df3
|
|||
, lig_dist_colname = LigDist_colname # from globals
|
||||
, tpos0 = 0 # 0 is a magic number that does my sensible default
|
||||
, 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$pos_count
|
||||
|
||||
|
||||
|
||||
|
||||
)
|
||||
{
|
||||
# Custom 2: x-axis geom tiles ~ lig distance
|
||||
|
||||
# order the df by position and ensure it is a factor
|
||||
|
||||
# order the df by position and ensure it is a factor
|
||||
plot_df = plot_df[order(plot_df[[xvar_colname]]), ]
|
||||
plot_df[[xvar_colname]] = factor(plot_df[[xvar_colname]])
|
||||
|
||||
|
|
@ -76,10 +79,18 @@ bp_stability_hmap <- function(plot_df = merged_df3
|
|||
#
|
||||
# Add col: 'group'
|
||||
plot_df$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$n=NULL
|
||||
|
||||
# check unique values in normalised data
|
||||
# cat("\nNo. of unique values in", stability_colname, "no rounding:"
|
||||
# , length(unique(plot_df[[stability_colname]])))
|
||||
# define a "max Y" in case the user didn't supply one
|
||||
if(reorder_position) {
|
||||
y_max = max(plot_df$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
|
||||
#subcols_ps
|
||||
|
|
@ -87,55 +98,63 @@ bp_stability_hmap <- function(plot_df = merged_df3
|
|||
|
||||
cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
|
||||
anno_bar=position_annotation(plot_df,
|
||||
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
|
||||
reorder_position=reorder_position,
|
||||
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
|
||||
)
|
||||
|
||||
# Generate the subcols barplot
|
||||
cowplot::plot_grid(
|
||||
ggplot(plot_df, aes_string(x = xvar_colname
|
||||
#, ordered = T
|
||||
)
|
||||
) +
|
||||
geom_bar(aes(fill = group)
|
||||
, colour = "grey", size=0.125) +
|
||||
|
||||
scale_fill_manual( values = subcols_bp_hmap
|
||||
, guide = "none") +
|
||||
# scale_x_discrete("Position", labels=factor(plot_df$position)) +
|
||||
|
||||
theme(
|
||||
panel.grid = element_line(color="lightgrey", size=0.125)
|
||||
, axis.text.x = element_text(size = my_xaxls
|
||||
subcols_plot = ggplot(plot_df) +
|
||||
scale_fill_manual( values = subcols_bp_hmap
|
||||
, guide = "none") +
|
||||
# scale_x_discrete("Position", labels=factor(plot_df$position)) +
|
||||
scale_y_continuous(limits=c(0,y_axis_limit)) +
|
||||
theme(
|
||||
panel.grid = element_line(color="lightgrey", size=0.125)
|
||||
, axis.text.x = element_text(size = my_xaxls
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
, axis.text.y = element_text(size = my_yaxls
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_blank()
|
||||
, axis.ticks = element_blank()
|
||||
#, axis.title.x = element_text(size = my_xaxts)
|
||||
, axis.title.y = element_text(size = my_yaxts )
|
||||
, plot.title = element_text(size = my_pts
|
||||
, hjust = 0.5)
|
||||
# , panel.grid = element_blank()
|
||||
, panel.background = element_rect(fill = "transparent", colour=NA)
|
||||
) +
|
||||
labs(title = p_title
|
||||
, x = my_xlab
|
||||
, y = my_ylab),
|
||||
, axis.text.y = element_text(size = my_yaxls
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.x = element_blank()
|
||||
, axis.ticks = element_blank()
|
||||
#, axis.title.x = element_text(size = my_xaxts)
|
||||
, axis.title.y = element_text(size = my_yaxts )
|
||||
, plot.title = element_text(size = my_pts
|
||||
, hjust = 0.5)
|
||||
# , panel.grid = element_blank()
|
||||
, panel.background = element_rect(fill = "transparent", colour=NA)
|
||||
) +
|
||||
labs(title = p_title
|
||||
, x = my_xlab
|
||||
, 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,
|
||||
anno_bar,
|
||||
#generate_distance_legend(plot_df),
|
||||
ncol = 1,
|
||||
align = "v",
|
||||
rel_heights = c(6,-0.1,1)
|
||||
#rel_widths = c(9/10, 0.4/10)
|
||||
)
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -81,13 +81,11 @@ LogoPlotCustomH <- function(plot_df
|
|||
|
||||
|
||||
if (rm_empty_y){
|
||||
cat(paste0("Original Rows: ",nrow(plot_df)))
|
||||
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
|
||||
|
|
@ -98,8 +96,10 @@ LogoPlotCustomH <- function(plot_df
|
|||
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 = 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' !!!
|
||||
#y_max = max(plot_df[[log_colname]], na.rm = T)
|
||||
#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 = 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)
|
||||
|
||||
rownames(logo_dfP_wf) = logo_dfP_wf[,1]
|
||||
#rownames(logo_dfP_wf) = logo_dfP_wf[,1]
|
||||
#dim(logo_dfP_wf)
|
||||
|
||||
logo_dfP_wf = logo_dfP_wf[,-1]
|
||||
#logo_dfP_wf = logo_dfP_wf[,-1]
|
||||
#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)
|
||||
position_or = as.numeric(colnames(logo_dfP_wf))
|
||||
|
||||
|
|
@ -167,11 +177,12 @@ LogoPlotCustomH <- function(plot_df
|
|||
ggplot() +
|
||||
geom_logo(logo_dfP_wf
|
||||
, method = "custom"
|
||||
#, method = "bits"
|
||||
, col_scheme = my_logo_col
|
||||
, seq_type = "aa") +
|
||||
#ylab("my custom height") +
|
||||
theme( axis.ticks.x = element_blank()
|
||||
, axis.ticks.length = unit(0, "pt")
|
||||
theme( axis.ticks = element_blank()
|
||||
#, axis.ticks.length = unit(0, "pt")
|
||||
, axis.title.x = element_blank()
|
||||
# , axis.text.x = element_blank() # turn this off and the below on if you want to visually
|
||||
# verify positions.
|
||||
|
|
@ -206,10 +217,13 @@ LogoPlotCustomH <- function(plot_df
|
|||
, labels = position_or
|
||||
, limits = factor(1:length(position_or))) +
|
||||
|
||||
scale_y_continuous(y_lab
|
||||
, breaks = seq(0, (y_lim), by = y_axis_increment)
|
||||
#, labels = seq(0, (y_lim), by = y_axis_increment)
|
||||
, limits = c(0, y_lim)) +
|
||||
scale_y_continuous(y_lab,
|
||||
breaks = seq(0,
|
||||
(y_lim),
|
||||
by = y_axis_increment
|
||||
),
|
||||
limits = c(0, y_lim)
|
||||
) +
|
||||
labs(y=y_lab),
|
||||
position_annotation(plot_df,
|
||||
bg = theme_bgc,
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@
|
|||
# This plots position tiles for the (up to) three ligands as well as drug
|
||||
position_annotation=function(plot_df,
|
||||
bg="transparent",
|
||||
reorder_position = FALSE, # enable to reorder according to plot_df$pos_count
|
||||
aa_pos_drug=1:100,
|
||||
active_aa_pos=1:100,
|
||||
aa_pos_lig1=1:100,
|
||||
|
|
@ -47,65 +48,112 @@ position_annotation=function(plot_df,
|
|||
plot_df$col_bg3 = ifelse(plot_df[["position"]]%in%aa_pos_lig3
|
||||
, "purple", plot_df$col_bg3)
|
||||
|
||||
# the call to generate_distance_colour_map should probably be
|
||||
# wherever the outer DF is built, and not here.
|
||||
plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
|
||||
|
||||
heat_bar = ggplot(plot_df,
|
||||
aes(x=factor(position)) # THIS STUPID FUCKING FACTOR THING
|
||||
) +
|
||||
geom_tile(aes(y=0),
|
||||
fill=plot_df$ligD_colours) +
|
||||
heat_bar = ggplot(plot_df) + # THIS STUPID FUCKING FACTOR THING
|
||||
|
||||
# scale_x_discrete("Position", labels=factor(plot_df$position)) +
|
||||
theme_nothing() +
|
||||
theme(#axis.text.x = element_text(angle = 90, size = 6),
|
||||
title = element_blank()
|
||||
) + # enable for alignment debug
|
||||
labs(x = NULL, y = NULL) #end of distance-heat-bar
|
||||
#NULL,
|
||||
pos_tiles = ggplot(plot_df,
|
||||
aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
|
||||
)
|
||||
) +
|
||||
# geom_tile(aes(y = 0, fill = col_aa, colour = col_aa)
|
||||
# ) +
|
||||
geom_tile(aes(y = 1, fill = bg_all, colour = bg_all)
|
||||
) +
|
||||
geom_tile(aes(y = 2, fill = col_bg1, colour = col_bg1)
|
||||
) +
|
||||
geom_tile(aes(y = 3, fill = col_bg2, colour = col_bg2)
|
||||
) +
|
||||
geom_tile(aes(y = 4, fill = col_bg3, colour = col_bg3)
|
||||
) +
|
||||
) + # enable for alignment debug
|
||||
labs(x = NULL, y = NULL) +
|
||||
|
||||
#scale_x_discrete("Position", labels=factor(plot_df$position)) +
|
||||
scale_color_manual(values = c(
|
||||
"brown"="brown",
|
||||
"green"="#00ff00",
|
||||
"transparent"="transparent",
|
||||
"slategrey"="#2f4f4f",
|
||||
"navyblue"="#000080",
|
||||
"purple"="#a020f0"
|
||||
),
|
||||
#expand=c(0,0)
|
||||
) +
|
||||
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)
|
||||
|
||||
heat_legend=get_legend(heat_bar)
|
||||
# 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,
|
||||
if(reorder_position) {
|
||||
pos_tiles = ggplot(plot_df) +
|
||||
#scale_x_discrete("Position", labels=factor(plot_df$position)) +
|
||||
scale_color_manual(values = c(
|
||||
"brown"="brown",
|
||||
"green"="#00ff00",
|
||||
"transparent"="transparent",
|
||||
"slategrey"="#2f4f4f",
|
||||
"navyblue"="#000080",
|
||||
"purple"="#a020f0"
|
||||
),
|
||||
#expand=c(0,0)
|
||||
) +
|
||||
scale_fill_manual(values = c(
|
||||
"brown"="brown",
|
||||
"green"="#00ff00",
|
||||
"transparent"="transparent",
|
||||
"slategrey"="#2f4f4f",
|
||||
"navyblue"="#000080",
|
||||
"purple"="#a020f0"
|
||||
),
|
||||
#expand=c(0,0)
|
||||
) +
|
||||
theme_nothing() +
|
||||
theme(plot.background = element_rect(fill = bg, colour=NA),
|
||||
#plot.margin = margin(t=0,b=0),
|
||||
panel.background = element_rect(fill = bg, colour=NA),
|
||||
legend.position = "none"
|
||||
) +
|
||||
labs(x = NULL, y= NULL) +
|
||||
geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all)
|
||||
) +
|
||||
geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
|
||||
) +
|
||||
geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
|
||||
) +
|
||||
geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
|
||||
)
|
||||
|
||||
} else {
|
||||
pos_tiles = ggplot(plot_df) +
|
||||
#scale_x_discrete("Position", labels=factor(plot_df$position)) +
|
||||
scale_color_manual(values = c(
|
||||
"brown"="brown",
|
||||
"green"="#00ff00",
|
||||
"transparent"="transparent",
|
||||
"slategrey"="#2f4f4f",
|
||||
"navyblue"="#000080",
|
||||
"purple"="#a020f0"
|
||||
),
|
||||
#expand=c(0,0)
|
||||
) +
|
||||
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=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)
|
||||
out_plot=cowplot::plot_grid(
|
||||
heat_bar,
|
||||
NULL,
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue