added new layput for dm_om and facet_lineage plot
This commit is contained in:
parent
a5b03e53e8
commit
375cdc2068
1 changed files with 90 additions and 22 deletions
|
|
@ -146,6 +146,7 @@ check = u2[!u2%in%u]; print(check)
|
|||
# lineage: labels
|
||||
# from "plyr"
|
||||
#==================
|
||||
#{Result:No of samples in selected lineages}
|
||||
table(df_lin$lineage)
|
||||
|
||||
df_lin$lineage_labels = mapvalues(df_lin$lineage
|
||||
|
|
@ -166,6 +167,19 @@ table(df_lin$mutation_info_labels)
|
|||
|
||||
table(df_lin$mutation_info) == table(df_lin$mutation_info_labels)
|
||||
|
||||
|
||||
#========================
|
||||
# duet_outcome: labels
|
||||
#========================
|
||||
#{Result: No. of D and S mutations in selected lineages}
|
||||
table(df_lin$duet_outcome)
|
||||
|
||||
df_lin$duet_outcome_labels = ifelse(df_lin$duet_outcome == "Destabilising", "D", "S")
|
||||
table(df_lin$duet_outcome_labels)
|
||||
|
||||
table(df_lin$duet_outcome) == table(df_lin$duet_outcome_labels)
|
||||
|
||||
|
||||
#=======================
|
||||
# subset dr muts only
|
||||
#=======================
|
||||
|
|
@ -208,28 +222,37 @@ my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcs
|
|||
# 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)
|
||||
# y = duet_outcome
|
||||
# fill = duet_scaled
|
||||
# Facet: Lineage
|
||||
#=======================================
|
||||
# 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)
|
||||
#plot_lineage_dist_duet_f paste0(plotdir,"/", "lineage_dist_duet_f.svg")
|
||||
#plot_lineage_dist_duet_f
|
||||
#svg(plot_lineage_dist_duet_f)
|
||||
|
||||
p1 = ggplot(df, aes(x = duet_scaled
|
||||
, y = lineage_labels))+
|
||||
, y = duet_outcome))+
|
||||
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 = my_palette, name = "DUET") +
|
||||
scale_fill_gradientn(colours = my_palette
|
||||
, name = "DUET"
|
||||
#, breaks = c(-1, 0, 1)
|
||||
#, labels = c(-1,0,1)
|
||||
#, limits = c(-1,1)
|
||||
) +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
|
||||
#, axis.text.y = element_blank()
|
||||
, axis.text.y = element_text(size = my_ats)
|
||||
, axis.title.x = element_text(size = my_ats)
|
||||
, axis.title.y = element_blank()
|
||||
|
|
@ -237,18 +260,19 @@ p1 = ggplot(df, aes(x = duet_scaled
|
|||
, plot.title = element_blank()
|
||||
, strip.text = 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", )+
|
||||
#, legend.title = element_text(size = my_als-6)
|
||||
, legend.title = element_blank()
|
||||
, legend.position = c(-0.08, 0.41)
|
||||
#, legend.direction = "horizontal"
|
||||
#, legend.position = "left"
|
||||
)+
|
||||
labs(x = "DUET")
|
||||
|
||||
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)))
|
||||
|
||||
#p1_copy
|
||||
#p1_with_legend = p1 + guides(fill = guide_colourbar(label = FALSE))
|
||||
|
||||
#=======================================
|
||||
# Plot 2: lineage dist: geom_density_ridges, allows alpha to be set
|
||||
# x = duet_scaled
|
||||
|
|
@ -279,14 +303,55 @@ p2 = ggplot(df, aes(x = duet_scaled
|
|||
, axis.ticks.y = element_blank()
|
||||
, plot.title = element_blank()
|
||||
, strip.text = element_text(size = my_als)
|
||||
, legend.text = element_text(size = my_als-2)
|
||||
, legend.title = element_text(size = my_als-3)
|
||||
, legend.text = element_text(size = my_als-4)
|
||||
, legend.title = element_text(size = my_als-4)
|
||||
, legend.position = c(0.8, 0.9)) +
|
||||
labs(x = "DUET"
|
||||
, fill = "Mutation class") # legend title
|
||||
|
||||
p2
|
||||
|
||||
#=======================================
|
||||
# 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 = 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)
|
||||
|
||||
p3 = ggplot(df, aes(x = duet_scaled
|
||||
, y = lineage_labels))+
|
||||
geom_density_ridges_gradient(aes(fill = ..x..)
|
||||
#, jittered_points = TRUE
|
||||
, scale = 3
|
||||
, size = 0.3 ) +
|
||||
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_text(size = my_ats)
|
||||
, 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-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")
|
||||
|
||||
p3
|
||||
|
||||
########################################################################
|
||||
#==============
|
||||
# combine plots
|
||||
|
|
@ -307,11 +372,14 @@ plot_lineage_dist_combined_dm_om_L
|
|||
svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6)
|
||||
|
||||
OutPlot2 = cowplot::plot_grid(p1, p2
|
||||
, labels = c("(a)", "(b)")
|
||||
, rel_widths = c(0.5/2, 0.5/2)
|
||||
, label_size = my_als)
|
||||
, labels = c("(a)", "(b)")
|
||||
#, label_x = -0.045, label_y = 0.92
|
||||
#, hjust = -0.7, vjust = -0.5
|
||||
#, align = "h"
|
||||
, rel_widths = c(0.5/2, 0.5/2)
|
||||
, label_size = my_als)
|
||||
|
||||
print(OutPlot2)
|
||||
dev.off()
|
||||
|
||||
##############################################################################
|
||||
##############################################################################
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue