added combined lineage plot
This commit is contained in:
parent
fe292e3717
commit
94454d6fba
10 changed files with 421 additions and 190 deletions
|
|
@ -32,37 +32,30 @@ outdir_images = paste0("~/git/Writing/thesis/images/results/"
|
|||
cat("plots will output to:", outdir_images)
|
||||
|
||||
###########################################################
|
||||
df3 = merged_df3
|
||||
# FIXME: port to a common script
|
||||
#=================
|
||||
# PREFORMATTING: for consistency
|
||||
#=================
|
||||
df3$sensitivity = ifelse(df3$dst_mode == 1, "R", "S")
|
||||
table(df3$sensitivity)
|
||||
# get from preformatting.R
|
||||
#df3
|
||||
|
||||
|
||||
# ConSurf labels
|
||||
consurf_colOld = "consurf_colour_rev"
|
||||
consurf_colNew = "consurf_outcome"
|
||||
df3[[consurf_colNew]] = df3[[consurf_colOld]]
|
||||
df3[[consurf_colNew]] = as.factor(df3[[consurf_colNew]])
|
||||
df3[[consurf_colNew]]
|
||||
levels(df3$consurf_outcome) = c( "nsd", 1, 2, 3, 4, 5, 6, 7, 8, 9)
|
||||
levels(df3$consurf_outcome)
|
||||
|
||||
# consurf_colOld = "consurf_colour_rev"
|
||||
# consurf_colNew = "consurf_outcome"
|
||||
# df3[[consurf_colNew]] = df3[[consurf_colOld]]
|
||||
# df3[[consurf_colNew]] = as.factor(df3[[consurf_colNew]])
|
||||
# df3[[consurf_colNew]]
|
||||
consurf_colname = "consurf_outcome"
|
||||
levels(df3[[consurf_colname]])
|
||||
|
||||
# SNAP2 labels
|
||||
snap2_colname = "snap2_outcome"
|
||||
df3[[snap2_colname]] <- str_replace(df3[[snap2_colname]], "effect", "Effect")
|
||||
df3[[snap2_colname]] <- str_replace(df3[[snap2_colname]], "neutral", "Neutral")
|
||||
levels(df3[[snap2_colname]])
|
||||
|
||||
##############################################################
|
||||
gene_all_cols = colnames(df3)[colnames(df3)%in%all_cols]
|
||||
|
||||
gene_outcome_cols = colnames(df3)[colnames(df3)%in%c(outcome_cols_stability
|
||||
, outcome_cols_affinity
|
||||
, outcome_cols_conservation)]
|
||||
gene_outcome_cols
|
||||
|
||||
|
||||
#=======================================================================
|
||||
#------------------------------
|
||||
# stability barplots:
|
||||
|
|
@ -129,45 +122,45 @@ dynamut2P = stability_count_bp(plotdf = df3
|
|||
|
||||
dynamut2P
|
||||
|
||||
# extract common legend
|
||||
common_legend = get_legend(duetP +
|
||||
guides(color = guide_legend(nrow = 1)) +
|
||||
theme(legend.position = "top"))
|
||||
|
||||
#==========================
|
||||
# output: STABILITY PLOTS
|
||||
#===========================
|
||||
bp_stability_CLP = paste0(outdir_images
|
||||
, tolower(gene)
|
||||
,"_bp_stability_CL.svg")
|
||||
|
||||
svg(bp_stability_CLP, width = 15, height = 12)
|
||||
print(paste0("plot filename:", bp_stability_CLP))
|
||||
|
||||
cowplot::plot_grid(
|
||||
common_legend,
|
||||
cowplot::plot_grid(duetP, foldxP
|
||||
, deepddgP, dynamut2P
|
||||
, nrow = 2
|
||||
, ncol = 2
|
||||
#, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
, labels = "AUTO"
|
||||
, label_size = 25)
|
||||
, ncol = 1
|
||||
, nrow = 2
|
||||
, rel_heights = c(0.4/10,9/10))
|
||||
|
||||
dev.off()
|
||||
# # extract common legend
|
||||
# common_legend = get_legend(duetP +
|
||||
# guides(color = guide_legend(nrow = 1)) +
|
||||
# theme(legend.position = "top"))
|
||||
#
|
||||
# #==========================
|
||||
# #output: STABILITY PLOTS
|
||||
# #===========================
|
||||
# bp_stability_CLP = paste0(outdir_images
|
||||
# , tolower(gene)
|
||||
# ,"_bp_stability_CL.svg")
|
||||
#
|
||||
# svg(bp_stability_CLP, width = 15, height = 12)
|
||||
# print(paste0("plot filename:", bp_stability_CLP))
|
||||
#
|
||||
# cowplot::plot_grid(
|
||||
# common_legend,
|
||||
# cowplot::plot_grid(duetP, foldxP
|
||||
# , deepddgP, dynamut2P
|
||||
# , nrow = 2
|
||||
# , ncol = 2
|
||||
# #, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
# , labels = "AUTO"
|
||||
# , label_size = 25)
|
||||
# , ncol = 1
|
||||
# , nrow = 2
|
||||
# , rel_heights = c(0.4/10,9/10))
|
||||
#
|
||||
# dev.off()
|
||||
###########################################################
|
||||
#=========================
|
||||
# Affinity outcome
|
||||
# check this var: outcome_cols_affinity
|
||||
# get from preformatting or put in globals
|
||||
#==========================
|
||||
DistCutOff = 10
|
||||
DistCutOff
|
||||
LigDist_colname # = "ligand_distance" # from globals
|
||||
ppi2Dist_colname = "interface_dist"
|
||||
naDist_colname = "TBC"
|
||||
ppi2Dist_colname
|
||||
naDist_colname
|
||||
|
||||
###########################################################
|
||||
# get plotting data within the distance
|
||||
|
|
@ -231,37 +224,37 @@ ppi2P = stability_count_bp(plotdf = df3_ppi2
|
|||
, bp_plot_title = paste(common_bp_title, "interface")
|
||||
)
|
||||
|
||||
# extract common legend
|
||||
common_legend_aff = get_legend(mLigP +
|
||||
guides(color = guide_legend(nrow = 1)) +
|
||||
theme(legend.position = "top"))
|
||||
|
||||
#==========================
|
||||
# output: AFFINITY PLOTS
|
||||
#==========================
|
||||
bp_affinity_CLP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_bp_affinity_CL.svg" )
|
||||
|
||||
print(paste0("plot filename:", bp_stability_CLP))
|
||||
svg(bp_affinity_CLP, width = 15, height = 6.5)
|
||||
|
||||
cowplot::plot_grid(
|
||||
common_legend,
|
||||
cowplot::plot_grid(mLigP, mmLigP
|
||||
, ppi2P
|
||||
, nrow = 1
|
||||
, ncol = 3
|
||||
#, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
, labels = "AUTO"
|
||||
, label_size = 25)
|
||||
, ncol = 1
|
||||
, nrow = 2
|
||||
, rel_heights = c(0.4/10,9/10))
|
||||
#, rel_widths = c(1,1,1))
|
||||
|
||||
|
||||
dev.off()
|
||||
# # extract common legend
|
||||
# common_legend_aff = get_legend(mLigP +
|
||||
# guides(color = guide_legend(nrow = 1)) +
|
||||
# theme(legend.position = "top"))
|
||||
#
|
||||
# #==========================
|
||||
# # output: AFFINITY PLOTS
|
||||
# #==========================
|
||||
# bp_affinity_CLP = paste0(outdir_images
|
||||
# ,tolower(gene)
|
||||
# ,"_bp_affinity_CL.svg" )
|
||||
#
|
||||
# print(paste0("plot filename:", bp_stability_CLP))
|
||||
# svg(bp_affinity_CLP, width = 15, height = 6.5)
|
||||
#
|
||||
# cowplot::plot_grid(
|
||||
# common_legend,
|
||||
# cowplot::plot_grid(mLigP, mmLigP
|
||||
# , ppi2P
|
||||
# , nrow = 1
|
||||
# , ncol = 3
|
||||
# #, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
# , labels = "AUTO"
|
||||
# , label_size = 25)
|
||||
# , ncol = 1
|
||||
# , nrow = 2
|
||||
# , rel_heights = c(0.4/10,9/10))
|
||||
# #, rel_widths = c(1,1,1))
|
||||
#
|
||||
#
|
||||
# dev.off()
|
||||
|
||||
################################################################
|
||||
#=========================
|
||||
|
|
@ -269,6 +262,21 @@ dev.off()
|
|||
# check this var:
|
||||
outcome_cols_conservation
|
||||
#==========================
|
||||
# consurf
|
||||
consurfP = stability_count_bp(plotdf = df3
|
||||
, df_colname = "consurf_outcome"
|
||||
#, leg_title = "ConSurf"
|
||||
#, label_categories = labels_consurf
|
||||
, yaxis_title = "Number of nsSNPs"
|
||||
, leg_position = "top"
|
||||
, subtitle_text = "ConSurf"
|
||||
, geom_ls = 5
|
||||
, bar_fill_values = consurf_colours # from globals
|
||||
, sts = sts
|
||||
, subtitle_colour= subtitle_colour)
|
||||
|
||||
consurfP
|
||||
|
||||
# provean
|
||||
proveanP = stability_count_bp(plotdf = df3
|
||||
, df_colname = "provean_outcome"
|
||||
|
|
@ -278,73 +286,172 @@ proveanP = stability_count_bp(plotdf = df3
|
|||
, leg_position = "top"
|
||||
, subtitle_text = "PROVEAN"
|
||||
, geom_ls = geom_ls
|
||||
, bar_fill_values = c("#F8766D", "#00BFC4")
|
||||
, bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep
|
||||
, sts = sts
|
||||
, subtitle_colour= subtitle_colour)
|
||||
|
||||
|
||||
# snap2
|
||||
snap2P = stability_count_bp(plotdf = df3
|
||||
, df_colname = "snap2_outcome"
|
||||
#, leg_title = "SNAP2"
|
||||
#, label_categories = labels_snap2
|
||||
, yaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = ""
|
||||
, leg_position = "top"
|
||||
, subtitle_text = "SNAP2"
|
||||
, geom_ls = geom_ls
|
||||
, bar_fill_values = c("#F8766D", "#00BFC4")
|
||||
, bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep
|
||||
, sts = sts
|
||||
, subtitle_colour= subtitle_colour)
|
||||
|
||||
# consurf
|
||||
consurfP = stability_count_bp(plotdf = df3
|
||||
, df_colname = "consurf_outcome"
|
||||
#, leg_title = "ConSurf"
|
||||
#, label_categories = labels_consurf
|
||||
, yaxis_title = ""
|
||||
, leg_position = "top"
|
||||
, subtitle_text = "ConSurf"
|
||||
, geom_ls = 5
|
||||
, bar_fill_values = consurf_colours # from globals
|
||||
, sts = sts
|
||||
, subtitle_colour= subtitle_colour)
|
||||
|
||||
consurfP
|
||||
#============================
|
||||
# output: CONSERVATION PLOTS
|
||||
#============================
|
||||
bp_conservation_CLP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_bp_conservation_CL.svg" )
|
||||
# bp_conservation_CLP = paste0(outdir_images
|
||||
# ,tolower(gene)
|
||||
# ,"_bp_conservation_CL.svg" )
|
||||
#
|
||||
# print(paste0("plot filename:", bp_conservation_CLP))
|
||||
# svg(bp_conservation_CLP, width = 15, height = 6.5)
|
||||
#
|
||||
# cowplot::plot_grid(proveanP, snap2P, consurfP
|
||||
# , nrow = 1
|
||||
# , ncol = 3
|
||||
# #, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
# , labels = "AUTO"
|
||||
# , label_size = 25
|
||||
# #, rel_heights = c(0.4/10,9/10))
|
||||
# , rel_widths = c(0.9, 0.9, 1.1))
|
||||
#
|
||||
#
|
||||
# dev.off()
|
||||
#####################################################################
|
||||
# LAYOUT
|
||||
my_label_size = 25
|
||||
#ratio 11.69 by 8.27
|
||||
w = 8.27*2
|
||||
h = 11.69*2
|
||||
|
||||
print(paste0("plot filename:", bp_conservation_CLP))
|
||||
svg(bp_conservation_CLP, width = 15, height = 6.5)
|
||||
|
||||
cowplot::plot_grid(proveanP, snap2P, consurfP
|
||||
, nrow = 1
|
||||
, ncol = 3
|
||||
#, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
, labels = "AUTO"
|
||||
, label_size = 25
|
||||
#, rel_heights = c(0.4/10,9/10))
|
||||
, rel_widths = c(0.9, 0.9, 1.1))
|
||||
tit1 = "Stability outcome"
|
||||
tit2 = "Affinity outcome"
|
||||
tit3 = "Conservation outcome"
|
||||
|
||||
|
||||
theme_georgia <- function(...) {
|
||||
theme_gray(base_family = "sans", ...) +
|
||||
theme(plot.title = element_text(face = "bold"))
|
||||
}
|
||||
|
||||
|
||||
title_theme <- calc_element("plot.title", theme_georgia())
|
||||
|
||||
pt1 = ggdraw() +
|
||||
draw_label(
|
||||
tit1,
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
#size = title_theme$size
|
||||
size = 30
|
||||
)
|
||||
|
||||
pt2 = ggdraw() +
|
||||
draw_label(
|
||||
tit2,
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
size = 30
|
||||
)
|
||||
|
||||
pt3 = ggdraw() +
|
||||
draw_label(
|
||||
tit3,
|
||||
fontfamily = title_theme$family,
|
||||
fontface = title_theme$face,
|
||||
size = 30
|
||||
)
|
||||
|
||||
# extract common legend
|
||||
common_legend_outcome = get_legend(mLigP +
|
||||
guides(color = guide_legend(nrow = 1)) +
|
||||
theme(legend.position = "top"))
|
||||
|
||||
|
||||
#=============
|
||||
# Output plot
|
||||
#=============
|
||||
OutPlotBP = function(x){
|
||||
cowplot::plot_grid(
|
||||
cowplot::plot_grid(pt1,
|
||||
common_legend_outcome,
|
||||
cowplot::plot_grid( duetP, foldxP
|
||||
, deepddgP, dynamut2P
|
||||
, nrow = 2
|
||||
, ncol = 2
|
||||
, labels = c("A", "B", "C","D")
|
||||
, label_size = my_label_size
|
||||
)
|
||||
, ncol = 1
|
||||
, rel_heights = c(7, 3, 90)),
|
||||
|
||||
cowplot::plot_grid(pt2,
|
||||
cowplot::plot_grid(mLigP, mmLigP, ppi2P
|
||||
, nrow = 1
|
||||
, ncol = 3
|
||||
, labels = c("E","F", "G")
|
||||
, label_size = my_label_size
|
||||
)
|
||||
, ncol = 1
|
||||
, rel_heights = c(1, 9)),
|
||||
|
||||
cowplot::plot_grid(pt3,
|
||||
cowplot::plot_grid(consurfP, proveanP, snap2P
|
||||
, nrow = 1
|
||||
, ncol = 3
|
||||
, labels = c("H", "I", "J")
|
||||
, labels_x = 0.2
|
||||
, label_size = my_label_size
|
||||
, rel_widths = c(0.2, 0.2, 0.2)
|
||||
)
|
||||
, ncol = 1
|
||||
, rel_heights = c(0.07, 0.93)
|
||||
),
|
||||
|
||||
nrow = 3,
|
||||
rel_heights = c(0.58, 0.25, 0.27),
|
||||
align = "hv"
|
||||
)
|
||||
}
|
||||
|
||||
bp_all_CLP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_bp_all_CL.svg"); print(paste0("plot filename:", bp_all_CLP))
|
||||
|
||||
bp_all_CLP_png = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_bp_all_CL.png"); print(paste0("plot filename:", bp_all_CLP_png))
|
||||
|
||||
svg(bp_all_CLP, width = w, height = h)
|
||||
OutPlotBP()
|
||||
dev.off()
|
||||
|
||||
png(bp_all_CLP_png, width = w, height = h, units = "in", res = 300 )
|
||||
OutPlotBP()
|
||||
dev.off()
|
||||
|
||||
|
||||
#####################################################################
|
||||
#===============================================================
|
||||
# ------------------------------
|
||||
# bp site site count: ALL
|
||||
# <10 Ang ligand
|
||||
# ------------------------------
|
||||
|
||||
posC_all = site_snp_count_bp(plotdf = df3
|
||||
, df_colname = "position"
|
||||
, xaxis_title = ""
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = "Number of Sites"
|
||||
, subtitle_size = 20)
|
||||
|
||||
|
||||
# ------------------------------
|
||||
# bp site site count: mCSM-lig
|
||||
# < 10 Ang ligand
|
||||
|
|
@ -354,8 +461,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
|
|||
posC_lig = site_snp_count_bp(plotdf = df3_lig
|
||||
, df_colname = "position"
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = "" #+ annotate("text", x = 1.5, y = 2.2, label = "Text No. 1")
|
||||
|
||||
, yaxis_title = "Number of Sites"#+ annotate("text", x = 1.5, y = 2.2, label = "Text No. 1")
|
||||
, subtitle_text = paste0(common_bp_title, " ligand")
|
||||
, subtitle_size = 20
|
||||
, subtitle_colour = subtitle_colour)
|
||||
|
|
@ -366,8 +472,8 @@ posC_lig = site_snp_count_bp(plotdf = df3_lig
|
|||
|
||||
posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2
|
||||
, df_colname = "position"
|
||||
, xaxis_title = ""
|
||||
, yaxis_title = ""
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
, yaxis_title = "Number of Sites"
|
||||
, subtitle_text = paste0(common_bp_title, " interface")
|
||||
, subtitle_size = 20
|
||||
, subtitle_colour = subtitle_colour)
|
||||
|
|
@ -386,12 +492,13 @@ posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2
|
|||
# output: SITE SNP count:
|
||||
# all + affinity
|
||||
#==========================
|
||||
my_label_size = 25
|
||||
pos_count_combined_CLP = paste0(outdir_images
|
||||
,tolower(gene)
|
||||
,"_pos_count_PS_AFF.svg")
|
||||
|
||||
|
||||
svg(pos_count_combined_CLP, width = 15, height = 6.5)
|
||||
svg(pos_count_combined_CLP, width = 20, height = 5.5)
|
||||
print(paste0("plot filename:", pos_count_combined_CLP))
|
||||
|
||||
cowplot::plot_grid(posC_all, posC_lig, posC_ppi2
|
||||
|
|
@ -400,7 +507,9 @@ cowplot::plot_grid(posC_all, posC_lig, posC_ppi2
|
|||
, ncol = 3
|
||||
#, labels = c("(a)", "(b)", "(c)", "(d)")
|
||||
, labels = "AUTO"
|
||||
, label_size = 25)
|
||||
, label_size = my_label_size)
|
||||
|
||||
dev.off()
|
||||
|
||||
|
||||
#===============================================================
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue