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fix many plot functions to stop them using the "g=ggplot()" pattern,

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which annoyingly throws away lots of useful data that RShiny needs for
clickable plots. Also split the "flame bar" for ligand distance out into
separate functions in generate_distance_colour_map.R. This can now be
easily incorporated into any "wide" graph showing all positions.
This commit is contained in:
Tanushree Tunstall 2022-08-03 18:56:14 +01:00
parent e498d46f8b
commit bdbc97c40a
8 changed files with 1323 additions and 725 deletions
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80
scripts/functions/lineage_dist.R
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@ -16,7 +16,7 @@ lineage_distP <- function(plotdf
, all_lineages = F
, use_lineages = c("L1", "L2", "L3", "L4")
, with_facet = F
, facet_wrap_var = ""
, facet_wrap_var = "" # FIXME: document what this is for
, fill_categ = "mutation_info_labels"
, fill_categ_cols = c("#E69F00", "#999999")
, my_ats = 15 # axis text size
@ -30,46 +30,44 @@ lineage_distP <- function(plotdf
, leg_label = "")
{
if(!all_lineages){
plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,]
}
LinDistP = ggplot(plotdf, aes_string(x = x_axis
, y = y_axis))+
geom_density_ridges(aes_string(fill = fill_categ)
, scale = 3
, size = 0.3
, alpha = 0.8) +
scale_x_continuous(expand = c(0.01, 0.01)) +
#coord_cartesian( xlim = c(-1, 1)) +
scale_fill_manual(values = fill_categ_cols) +
theme(axis.text.x = element_text(size = my_ats
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_ats)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_blank()
, strip.text = element_text(size = my_strip_ts)
, legend.text = element_text(size = my_leg_ts)
, legend.title = element_text(size = my_leg_title)
, legend.position = c(0.8, 0.9)) +
labs(x = x_lab
, fill = leg_label)
if (with_facet){
# used reformulate or make as formula
#fwv = reformulate(facet_wrap_var)
fwv = as.formula(paste0("~", facet_wrap_var))
LinDistP = LinDistP +
if(!all_lineages){
plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,]
}
ggplot(plotdf, aes_string(x = x_axis
, y = y_axis))+
geom_density_ridges(aes_string(fill = fill_categ)
, scale = 3
, size = 0.3
, alpha = 0.8) +
scale_x_continuous(expand = c(0.01, 0.01)) +
#coord_cartesian( xlim = c(-1, 1)) +
scale_fill_manual(values = fill_categ_cols) +
theme(axis.text.x = element_text(size = my_ats
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_ats)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_blank()
, strip.text = element_text(size = my_strip_ts)
, legend.text = element_text(size = my_leg_ts)
, legend.title = element_text(size = my_leg_title)
, legend.position = c(0.8, 0.9)) +
labs(x = x_lab
, fill = leg_label) +
# FIXME: This didn't work BEFORE i fixed the ggplot() assignment thing!!!
if (with_facet){
# used reformulate or make as formula
#fwv = reformulate(facet_wrap_var)
fwv = as.formula(paste0("~", facet_wrap_var))
facet_wrap(fwv) +
theme(legend.position = leg_pos_wf
, legend.direction = leg_dir_wf)
}
return(LinDistP)
theme(legend.position = leg_pos_wf
, legend.direction = leg_dir_wf)
}
}