renamed file in scratch plot/
This commit is contained in:
parent
25f2f9e4a2
commit
b36bfc9e9d
1 changed files with 112 additions and 83 deletions
|
|
@ -179,14 +179,9 @@ table(my_df_other$lineage)
|
|||
########################################################################
|
||||
|
||||
#==========================
|
||||
# Plot 1: ALL Muts
|
||||
# x = mcsm_values, y = dist
|
||||
# fill = stability
|
||||
# Distribution plots
|
||||
#============================
|
||||
|
||||
#my_plot_name_dm_om = 'lineage_dist_DM_OM_PS.svg'
|
||||
#plot_lineage_dm_om_duet = paste0(plotdir,"/", my_plot_name_dm_om)
|
||||
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
# REASSIGNMENT
|
||||
df <- df_lin
|
||||
|
|
@ -200,73 +195,29 @@ rm(df_lin)
|
|||
# 2 : ggridges (good!)
|
||||
my_ats = 15 # axis text size
|
||||
my_als = 20 # axis label size
|
||||
|
||||
#=======================
|
||||
# Plot 1: lineage dist
|
||||
#=======================
|
||||
# check plot name
|
||||
plot_lineage_duet
|
||||
|
||||
n_colours = length(unique(df$duet_scaled))
|
||||
|
||||
#my_palette <- colorRampPalette(c(mcsm_red, "#f8766d", "white","#00bfc4", mcsm_blue))(n = 400)
|
||||
my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)
|
||||
|
||||
# output svg
|
||||
#svg(plot_lineage_duet)
|
||||
#=======================================
|
||||
# Plot 1: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!)
|
||||
# else same as geom_density_ridges)
|
||||
# x = duet_scaled
|
||||
# y = lineage_labels
|
||||
# fill = duet_scaled
|
||||
# NO FACET (nf)
|
||||
#=======================================
|
||||
# output individual svg
|
||||
#plot_lineage_dist_duet_nf = paste0(plotdir,"/", "lineage_dist_duet_nf.svg")
|
||||
#plot_lineage_dist_duet_nf
|
||||
#svg(plot_lineage_dist_duet_nf)
|
||||
|
||||
p1 = ggplot(df, aes(x = duet_scaled
|
||||
, y = duet_outcome))+
|
||||
, y = lineage_labels))+
|
||||
geom_density_ridges_gradient(aes(fill = ..x..)
|
||||
#, jittered_points = TRUE
|
||||
, scale = 3
|
||||
, size = 0.3 ) +
|
||||
facet_wrap( ~lineage_labels
|
||||
, scales = "free"
|
||||
#, labeller = labeller(lineage = my_labels)
|
||||
) +
|
||||
coord_cartesian( xlim = c(-1, 1)) +
|
||||
#scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
|
||||
# , name = "DUET" ) +
|
||||
#scale_fill_gradientn(colours = c(mcsm_red, "#f8766d", "white","#00bfc4", mcsm_blue)
|
||||
# , name = "DUET" ) +
|
||||
scale_fill_gradientn(colours = my_palette, name = "DUET") +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.x = element_blank()
|
||||
, axis.title.y = element_blank()
|
||||
, axis.ticks.y = element_blank()
|
||||
, plot.title = element_blank()
|
||||
, strip.text = element_text(size = my_als)
|
||||
, legend.text = element_text(size = my_als-6)
|
||||
, legend.title = element_text(size = my_als-3)
|
||||
)
|
||||
|
||||
print(p1)
|
||||
#dev.off()
|
||||
#=======================================
|
||||
# Plot 2: lineage dist by mutation_info
|
||||
#=======================================
|
||||
|
||||
p2 = ggplot(df, aes(x = duet_scaled
|
||||
, y = mutation_info_labels))+
|
||||
geom_density_ridges_gradient(aes(fill = ..x..)
|
||||
#, jittered_points = TRUE
|
||||
, scale = 3
|
||||
, size = 0.3 ) +
|
||||
facet_wrap(~lineage_labels
|
||||
#, scales = "free"
|
||||
#, labeller = labeller(lineage = my_labels)
|
||||
) +
|
||||
|
||||
coord_cartesian( xlim = c(-1, 1)) +
|
||||
#scale_fill_gradientn(colours = c("#ae301e", "white", "#007d85")
|
||||
# , name = "DUET" ) +
|
||||
#scale_fill_gradientn(colours = c("mcsm_red", "white", "mcsm_blue")
|
||||
# , name = "DUET" ) +
|
||||
scale_fill_gradientn(colours = my_palette, name = "DUET") +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
, angle = 90
|
||||
|
|
@ -274,26 +225,42 @@ p2 = ggplot(df, aes(x = duet_scaled
|
|||
, vjust = 0.4)
|
||||
|
||||
, axis.text.y = element_text(size = my_ats)
|
||||
, axis.title.x = element_blank()
|
||||
, axis.title.x = element_text(size = my_ats)
|
||||
, axis.title.y = element_blank()
|
||||
, axis.ticks.y = element_blank()
|
||||
, plot.title = element_blank()
|
||||
, strip.text = element_text(size = my_als)
|
||||
, legend.position = "none"
|
||||
#, legend.text = element_text(size = my_als-5)
|
||||
#, legend.title = element_text(size = my_als)
|
||||
)
|
||||
, legend.text = element_text(size = my_als-10)
|
||||
, legend.title = element_text(size = my_als-3)
|
||||
, legend.position = c(0.8, 0.8)) +
|
||||
#, legend.direction = "horizontal")+
|
||||
#, legend.position = "top", )+
|
||||
labs(x = "DUET")
|
||||
|
||||
print(p2)
|
||||
p1
|
||||
|
||||
#==============================
|
||||
#p1_copy = p1 + guides(fill = guide_colourbar(label = FALSE))
|
||||
#p1_copy= p1_copy + guides(size=guide_legend("Source", override.aes=list(shape=15, size = 10)))
|
||||
|
||||
p3 = ggplot(df, aes(x = duet_scaled
|
||||
#p1_copy
|
||||
#=======================================
|
||||
# Plot 2: lineage dist: geom_density_ridges, allows alpha to be set
|
||||
# x = duet_scaled
|
||||
# y = lineage_labels
|
||||
# fill = mutation_info
|
||||
# NO FACET
|
||||
#=======================================
|
||||
# output svg
|
||||
#plot_lineage_dist_duet_dm_om = paste0(plotdir,"/", "lineage_dist_duet_dm_om.svg")
|
||||
#plot_lineage_dist_duet_dm_om
|
||||
#svg(plot_lineage_dist_duet_dm_om)
|
||||
|
||||
p2 = ggplot(df, aes(x = duet_scaled
|
||||
, y = lineage_labels))+
|
||||
geom_density_ridges_gradient(aes(fill = factor(mutation_info_labels))
|
||||
#, jittered_points = TRUE
|
||||
geom_density_ridges(aes(fill = factor(mutation_info_labels))
|
||||
, scale = 3
|
||||
, size = 0.3 ) +
|
||||
, size = 0.3
|
||||
, alpha = 0.8) +
|
||||
coord_cartesian( xlim = c(-1, 1)) +
|
||||
scale_fill_manual(values = c("#E69F00", "#999999")) +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
|
|
@ -309,23 +276,85 @@ p3 = ggplot(df, aes(x = duet_scaled
|
|||
, legend.text = element_text(size = my_als-2)
|
||||
, legend.title = element_text(size = my_als-3)
|
||||
, legend.position = c(0.8, 0.9)) +
|
||||
labs(x = "DUET", fill = "Mutation class")
|
||||
labs(x = "DUET"
|
||||
, fill = "Mutation class") # legend title
|
||||
|
||||
# Modify legend titles
|
||||
#p + labs(fill = "Dose (mg)")
|
||||
|
||||
p3
|
||||
p2
|
||||
|
||||
########################################################################
|
||||
#==============
|
||||
# combine plot
|
||||
#===============
|
||||
|
||||
plot_lineage_dist_combined_dm_om
|
||||
svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6)
|
||||
|
||||
printFile = cowplot::plot_grid(p1, p3
|
||||
printFile = cowplot::plot_grid(p1, p2
|
||||
, rel_widths = c(0.5/2, 0.5/2)
|
||||
, label_size = my_als+10)
|
||||
|
||||
print(printFile)
|
||||
dev.off()
|
||||
|
||||
|
||||
########################################################################
|
||||
# alternate combination
|
||||
########################################################################
|
||||
#=======================
|
||||
# Plot 3: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!)
|
||||
# else same as geom_density_ridges)
|
||||
# x = duet_scaled
|
||||
# y = duet_outcome
|
||||
# FACET (f) = lineage
|
||||
#=======================
|
||||
|
||||
# output individual svg
|
||||
#plot_lineage_dist_duet = paste0(plotdir,"/", "lineage_dist_duet_f.svg")
|
||||
#plot_lineage_dist_duet
|
||||
#svg(plot_lineage_dist_duet)
|
||||
|
||||
p3 = ggplot(df, aes(x = duet_scaled
|
||||
, y = duet_outcome))+
|
||||
|
||||
geom_density_ridges_gradient(aes(fill = ..x..)
|
||||
, scale = 3
|
||||
, size = 0.3) +
|
||||
|
||||
facet_wrap( ~lineage_labels
|
||||
, scales = "free"
|
||||
#, labeller = labeller(lineage = my_labels) # sorted by lineage_labels
|
||||
) +
|
||||
coord_cartesian( xlim = c(-1, 1)) +
|
||||
scale_fill_gradientn(colours = my_palette, name = "DUET") +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.x = element_text(size = my_ats)
|
||||
, axis.title.y = element_blank()
|
||||
, axis.ticks.y = element_blank()
|
||||
, plot.title = element_blank()
|
||||
, strip.text = element_text(size = my_als)
|
||||
, legend.text = element_text(size = my_als-6)
|
||||
, legend.title = element_text(size = my_als-3))+
|
||||
labs(x = "DUET")
|
||||
|
||||
print(p3)
|
||||
#dev.off()
|
||||
|
||||
#==============
|
||||
# combine plot: alt version
|
||||
#===============
|
||||
plot_lineage_dist_duet_fandnf = paste0(plotdir,"/", "lineage_dist_duet_fandnf.svg")
|
||||
plot_lineage_dist_duet_fandnf
|
||||
svg(plot_lineage_dist_duet_fandnf, width = 12, height = 6)
|
||||
|
||||
printFile = cowplot::plot_grid(p3, p2
|
||||
, rel_widths = c(0.5/2, 0.5/2)
|
||||
, label_size = my_als+10)
|
||||
|
||||
print(printFile)
|
||||
dev.off()
|
||||
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue