generated ggpairs plots finally
This commit is contained in:
parent
b68841b337
commit
a3e5283a9b
11 changed files with 657 additions and 939 deletions
|
|
@ -4,7 +4,6 @@ posC_lig
|
|||
ppi2P
|
||||
posC_ppi2
|
||||
peP
|
||||
pe_allCL
|
||||
|
||||
|
||||
theme_georgia <- function(...) {
|
||||
|
|
@ -22,12 +21,127 @@ common_legend_outcome = get_legend(mLigP +
|
|||
guides(color = guide_legend(nrow = 1)) +
|
||||
theme(legend.position = "top"))
|
||||
|
||||
###############################################################
|
||||
# ###############################################################
|
||||
# #================================
|
||||
# # Lig Affinity: outcome + site
|
||||
# #================================
|
||||
# ligT = paste0(common_bp_title, " ligand")
|
||||
# lig_affT = ggdraw() +
|
||||
# draw_label(
|
||||
# ligT,
|
||||
# fontfamily = title_theme$family,
|
||||
# fontface = title_theme$face,
|
||||
# #size = title_theme$size
|
||||
# size = 8
|
||||
# )
|
||||
|
||||
# #-------------
|
||||
# # Outplot
|
||||
# #-------------
|
||||
# ligaffP = paste0(outdir_images
|
||||
# ,tolower(gene)
|
||||
# ,"_lig_oc.png")
|
||||
#
|
||||
# #svg(affP, width = 20, height = 5.5)
|
||||
# print(paste0("plot filename:", ligaffP))
|
||||
# png(ligaffP, units = "in", width = 6, height = 4, res = 300 )
|
||||
# cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome,
|
||||
# nrow = 2,
|
||||
# rel_heights = c(1,1)
|
||||
# ),
|
||||
# cowplot::plot_grid(mLigP, mmLigP, posC_lig
|
||||
# , nrow = 1
|
||||
# #, labels = c("A", "B", "C","D")
|
||||
# , rel_widths = c(1,1,1.8)
|
||||
# , align = "h"),
|
||||
# nrow = 2,
|
||||
# labels = c("A", ""),
|
||||
# label_size = 12,
|
||||
# rel_heights = c(1,8))
|
||||
# dev.off()
|
||||
# #############################################################
|
||||
# #================================
|
||||
# # PPI2 Affinity: outcome + site
|
||||
# #================================
|
||||
# ppi2T = paste0(common_bp_title, " PP-interface")
|
||||
# ppi2_affT = ggdraw() +
|
||||
# draw_label(
|
||||
# ppi2T,
|
||||
# fontfamily = title_theme$family,
|
||||
# fontface = title_theme$face,
|
||||
# #size = title_theme$size
|
||||
# size = 8
|
||||
# )
|
||||
#
|
||||
#
|
||||
# #-------------
|
||||
# # Outplot: PPI2
|
||||
# #-------------
|
||||
# ppiaffP = paste0(outdir_images
|
||||
# ,tolower(gene)
|
||||
# ,"_ppi2_oc.png")
|
||||
#
|
||||
# #svg(affP, width = 20, height = 5.5)
|
||||
# print(paste0("plot filename:", ppiaffP))
|
||||
# png(ppiaffP, units = "in", width = 6, height = 4, res = 300 )
|
||||
#
|
||||
#
|
||||
# cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome,
|
||||
# nrow = 2,
|
||||
# rel_heights = c(1,1)),
|
||||
# cowplot::plot_grid(ppi2P, posC_ppi2
|
||||
# , nrow = 1
|
||||
# , rel_widths = c(1.2,1.8)
|
||||
# , align = "h"
|
||||
# , label_size = my_label_size),
|
||||
# nrow = 2,
|
||||
# labels = c("B", ""),
|
||||
# label_size = 12,
|
||||
# rel_heights = c(1,8)
|
||||
# )
|
||||
#
|
||||
# dev.off()
|
||||
# #############################################################
|
||||
#peP # pe counts
|
||||
#================================
|
||||
# Lig Affinity: outcome + site
|
||||
# PE + All position count
|
||||
#================================
|
||||
# peT_allT = ggdraw() +
|
||||
# draw_label(
|
||||
# paste0("All mutation sites"),
|
||||
# fontfamily = title_theme$family,
|
||||
# fontface = title_theme$face,
|
||||
# #size = title_theme$size
|
||||
# size = 8
|
||||
# )
|
||||
# #------------------------
|
||||
# # Outplot: lig+ppi2+pe
|
||||
# #------------------------
|
||||
# pe_allCL = paste0(outdir_images
|
||||
# ,tolower(gene)
|
||||
# ,"_pe_oc.png")
|
||||
#
|
||||
# #svg(affP, width = 20, height = 5.5)
|
||||
# print(paste0("plot filename:", pe_allCL))
|
||||
# png(pe_allCL, units = "in", width = 6, height = 4, res = 300 )
|
||||
#
|
||||
#
|
||||
# cowplot::plot_grid(peT_allT,
|
||||
# cowplot::plot_grid(peP, posC_all
|
||||
# , nrow = 1
|
||||
# , rel_widths = c(1, 2)
|
||||
# , align = "h"),
|
||||
# nrow = 2,
|
||||
# labels = c("C", "", ""),
|
||||
# label_size = 12,
|
||||
# rel_heights = c(1,8))
|
||||
#
|
||||
# dev.off()
|
||||
#===========================================
|
||||
# COMBINE ALL three
|
||||
#==========================================
|
||||
ligT = paste0(common_bp_title, " ligand")
|
||||
lig_affT = ggdraw() +
|
||||
lig_affT = ggdraw() +
|
||||
draw_label(
|
||||
ligT,
|
||||
fontfamily = title_theme$family,
|
||||
|
|
@ -36,113 +150,6 @@ lig_affT = ggdraw() +
|
|||
size = 8
|
||||
)
|
||||
|
||||
#-------------
|
||||
# Outplot
|
||||
#-------------
|
||||
ligaffP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_lig_oc.png")
|
||||
|
||||
#svg(affP, width = 20, height = 5.5)
|
||||
print(paste0("plot filename:", ligaffP))
|
||||
png(ligaffP, units = "in", width = 6, height = 4, res = 300 )
|
||||
cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome,
|
||||
nrow = 2,
|
||||
rel_heights = c(1,1)
|
||||
),
|
||||
cowplot::plot_grid(mLigP, mmLigP, posC_lig
|
||||
, nrow = 1
|
||||
#, labels = c("A", "B", "C","D")
|
||||
, rel_widths = c(1,1,1.8)
|
||||
, align = "h"),
|
||||
nrow = 2,
|
||||
labels = c("A", ""),
|
||||
label_size = 12,
|
||||
rel_heights = c(1,8))
|
||||
dev.off()
|
||||
#############################################################
|
||||
#================================
|
||||
# PPI2 Affinity: outcome + site
|
||||
#================================
|
||||
ppi2T = paste0(common_bp_title, " PP-interface")
|
||||
ppi2_affT = ggdraw() +
|
||||
draw_label(
|
||||
ppi2T,
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
#size = title_theme$size
|
||||
size = 8
|
||||
)
|
||||
|
||||
|
||||
#-------------
|
||||
# Outplot: PPI2
|
||||
#-------------
|
||||
ppiaffP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_ppi2_oc.png")
|
||||
|
||||
#svg(affP, width = 20, height = 5.5)
|
||||
print(paste0("plot filename:", ppiaffP))
|
||||
png(ppiaffP, units = "in", width = 6, height = 4, res = 300 )
|
||||
|
||||
|
||||
cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome,
|
||||
nrow = 2,
|
||||
rel_heights = c(1,1)),
|
||||
cowplot::plot_grid(ppi2P, posC_ppi2
|
||||
, nrow = 1
|
||||
, rel_widths = c(1.2,1.8)
|
||||
, align = "h"
|
||||
, label_size = my_label_size),
|
||||
nrow = 2,
|
||||
labels = c("B", ""),
|
||||
label_size = 12,
|
||||
rel_heights = c(1,8)
|
||||
)
|
||||
|
||||
dev.off()
|
||||
#############################################################
|
||||
peP # pe counts
|
||||
#================================
|
||||
# PE + All position count
|
||||
#================================
|
||||
peT_allT = ggdraw() +
|
||||
draw_label(
|
||||
paste0("All mutation sites"),
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
#size = title_theme$size
|
||||
size = 8
|
||||
)
|
||||
|
||||
|
||||
#-------------
|
||||
# Outplot: PPI2
|
||||
#-------------
|
||||
pe_allCL = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_pe_oc.png")
|
||||
|
||||
#svg(affP, width = 20, height = 5.5)
|
||||
print(paste0("plot filename:", pe_allCL))
|
||||
png(pe_allCL, units = "in", width = 6, height = 4, res = 300 )
|
||||
|
||||
|
||||
cowplot::plot_grid(peT_allT,
|
||||
cowplot::plot_grid(peP, posC_all
|
||||
, nrow = 1
|
||||
, rel_widths = c(1, 2)
|
||||
, align = "h"),
|
||||
nrow = 2,
|
||||
labels = c("C", "", ""),
|
||||
label_size = 12,
|
||||
rel_heights = c(1,8))
|
||||
|
||||
dev.off()
|
||||
#===========================================
|
||||
# COMBINE ALL three
|
||||
#==========================================
|
||||
p1 = cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome, nrow=2),
|
||||
cowplot::plot_grid(mLigP, mmLigP, posC_lig
|
||||
, nrow = 1
|
||||
|
|
@ -152,8 +159,18 @@ p1 = cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome, nrow=
|
|||
rel_heights = c(1,8)
|
||||
|
||||
)
|
||||
|
||||
|
||||
#p1
|
||||
###########################################################
|
||||
ppi2T = paste0(common_bp_title, " PP-interface")
|
||||
ppi2_affT = ggdraw() +
|
||||
draw_label(
|
||||
ppi2T,
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
#size = title_theme$size
|
||||
size = 8
|
||||
)
|
||||
###########################################################
|
||||
p2 = cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome, nrow=2),
|
||||
cowplot::plot_grid(ppi2P, posC_ppi2
|
||||
, nrow = 1
|
||||
|
|
@ -162,7 +179,17 @@ p2 = cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome, nro
|
|||
nrow = 2,
|
||||
rel_heights = c(1,8)
|
||||
)
|
||||
|
||||
#p2
|
||||
###########################################################
|
||||
# PE + All position count
|
||||
peT_allT = ggdraw() +
|
||||
draw_label(
|
||||
paste0("All mutation sites"),
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
#size = title_theme$size
|
||||
size = 8
|
||||
)
|
||||
|
||||
p3 = cowplot::plot_grid(cowplot::plot_grid(peT_allT, nrow = 2
|
||||
, rel_widths = c(1,3),axis = "lr"),
|
||||
|
|
@ -174,16 +201,14 @@ p3 = cowplot::plot_grid(cowplot::plot_grid(peT_allT, nrow = 2
|
|||
axis = "lr",
|
||||
rel_heights = c(1,8)
|
||||
),
|
||||
rel_heights = c(1,10),
|
||||
rel_heights = c(1,18),
|
||||
nrow = 2,axis = "lr")
|
||||
|
||||
|
||||
|
||||
p3
|
||||
#===============
|
||||
# Final combine
|
||||
#===============
|
||||
w = 11.75
|
||||
h = 3.7
|
||||
w = 11.79
|
||||
h = 3.5
|
||||
mut_impact_CLP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_mut_impactCLP.png")
|
||||
|
|
@ -229,9 +254,21 @@ conCLP = paste0(outdir_images
|
|||
,tolower(gene)
|
||||
,"_consurf_BP.png")
|
||||
|
||||
print(paste0("plot filename:", sens_conP))
|
||||
png(sens_conP, units = "in", width = w, height = h, res = 300 )
|
||||
|
||||
print(paste0("plot filename:", conCLP))
|
||||
png(conCLP, units = "in", width = w, height = h, res = 300 )
|
||||
consurfP
|
||||
|
||||
dev.off()
|
||||
#================================
|
||||
# Sensitivity numbers: geom_tile
|
||||
#================================
|
||||
sensCLP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_sensN_tile.png")
|
||||
|
||||
print(paste0("plot filename:", sensCLP))
|
||||
png(sensCLP, units = "in", width = 1, height = 1, res = 300 )
|
||||
sensP
|
||||
dev.off()
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue