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6-shift_plots.R
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require(openxlsx)
require(ggplot2)
require(cowplot)
require(rogme)
my_plot_sf<-function(sf){
xplot<- seq(0.1, 0.9, 0.1)
yplot<- sf[[1]]$difference
ylim <- max(max(abs(sf[[1]]$ci_upper)), max(abs(sf[[1]]$ci_lower)))
ylim <- c(-ylim, ylim)
midpt <- (nrow(sf[[1]]) - 1)/2 + 1
xintercept<-0.5
yintercept<-0
sf.df <- data.frame("x" = xplot, "difference"= yplot)
sf.df$sign <- sign(sf.df$difference)
sf.df$ci_lower<- sf[[1]]$ci_lower
sf.df$ci_upper<- sf[[1]]$ci_upper
sf.df$deco <- c(seq(1, midpt), seq(midpt - 1, 1))
q_line_alpha <- 0.5
q_line_size <- 1.5
symb_fill = c("darkred", "darkblue")
symb_col <- c("black")
q_line_col <- "grey50"
theme2_alpha <- c(0.4, 1)
symb_size<-5
psf <- ggplot(sf.df, aes_string(x = xplot, y = "difference")) +
geom_hline(yintercept = 0, linetype = 2, alpha = 0.5) +
geom_vline(xintercept = xintercept, linetype = 2,
alpha = 0.5) + theme_bw() +
theme(axis.text.x = element_text(size = 14), axis.text.y = element_text(size = 14),
axis.title.x = element_text(size = 16, face = "bold"),
axis.title.y = element_text(size = 16, face = "bold")) +
scale_y_continuous(limits = ylim)
psf <- psf + geom_linerange(aes(ymin = ci_lower, ymax = ci_upper),
colour = "white", size = 0.5) +
geom_linerange(aes(ymin = ci_lower, ymax = ci_upper,
colour = factor(sign), alpha = factor(deco)),
size = 0.5) +
scale_color_manual(values = symb_fill, guide = FALSE) +
scale_alpha_discrete(range = theme2_alpha, guide = FALSE) +
geom_line(colour = q_line_col, alpha = q_line_alpha,
linetype = "solid", size = q_line_size) +
geom_point(colour = "black", fill = "white",
size = symb_size, shape = 21) +
geom_point(aes(fill = factor(sign),
alpha = factor(deco)),
colour = symb_col,
size = symb_size,
shape = 21) +
scale_fill_manual(values = symb_fill, guide = FALSE) +
scale_alpha_discrete(range = theme2_alpha, guide = FALSE)
psf
}
sub<-read.csv("data/ml_data.csv")
vars.interest<-names(sub)[c(1, 3:10)]
names.vars<- list("BRESLOW", "GM-CSF", "IL-4", "IL-6",
"IL-10", "IL-17A", "IFN-\u03b3",
"TGF-\u03b2","DCD")
names(names.vars)<-vars.interest
unit.vars<-list("mm", "pg/mL",
"pg/mL", "pg/mL",
"pg/mL", "pg/mL",
"pg/mL",
"ng/mL", "ng/mL")
names(unit.vars)<-vars.interest
for(newVar in vars.interest){
g1<-na.omit(sub[sub$EVOL_METASTASIS==0, newVar])
g2<-na.omit(sub[sub$EVOL_METASTASIS==1, newVar])
df <- mkt2(g1, g2)
# Compute shift function
sf <- shifthd_pbci(data = df, formula = obs ~ gr)
#PLOT DISTRIBUTION AND DECILES
p <- plot_scat2(df,
xlabel = "",
ylabel = unit.vars[newVar],
alpha = .3,
shape = 21,
colour = "grey10",
fill = "grey90")# scatterplots
p <- plot_hd_bars(p, col = "grey21", width = 0.5, q_size = 0.5,
md_size = 1.5)
p<-plot_hd_links(p, sf[[1]], link_col = c("darkred", "darkblue"))
p <- p +
coord_flip() + # flip axes
scale_x_discrete(labels=c("Group2" = "MET", "Group1" = "FREE")) +
theme(axis.text.x = element_text(size=15, face="bold"),
axis.text.y = element_text(size=15, face="bold"),
axis.title.y = element_text(size=25, face="bold")) +
ggtitle(names.vars[newVar]) +
theme(plot.title = element_text(size = 25, face="bold", hjust = 0.5))
save_plot(paste0("plots/deciles_", paste0(names.vars[newVar], ".svg")),
p, base_height = 7, base_width = 7)
## PLOT SHIFT FUNCTION
psf<-my_plot_sf(sf)
psf <- psf +
xlab("Group Deciles") +
ylab(paste0("FREE - MET \n decile difference \n",
paste0(paste0("(", unit.vars[newVar]), ")"))) +
scale_x_continuous(breaks = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9),
labels = c("1st", "2nd", "3rd", "4th", "5th \n (median)",
"6th", "7th", "8th", "9th"))
save_plot(paste0("plots/shift_", paste0(names.vars[newVar], ".svg")),
psf, base_height = 7, base_width = 7)
# Arrange both plots
both.p<-plot_grid(p, psf, ncol = 1, nrow = 2)
save_plot(paste0("plots/decile_shift_", paste0(names.vars[newVar], ".svg")),
both.p, base_height = 7, base_width = 7)
}