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combine fig2 and fig3
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@princyparsana
princyparsana committed Apr 22, 2019
1 parent 1bb8d3d commit ef24a71
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104 changes: 100 additions & 4 deletions publication_figures/src/makefig2.R
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Expand Up @@ -118,7 +118,7 @@ fig3 <- plot_grid(plot.blood + xlim(0.3,1.0) + ylim(0, 1) + theme(legend.positio
# plot.subcutaneous + xlim(0.3,1.0) + ylim(0, 1) + theme(legend.position="none"),
plot.thyroid + xlim(0.3,1.0) + ylim(0, 1) + theme(legend.position="none"),
align = 'vh',
labels = c("a", "b", "c"),
labels = c("d", "e", "f"),
hjust = -1,
nrow = 1
)
Expand All @@ -131,7 +131,103 @@ fig2b <- plot_grid( fig3, legend, rel_widths = c(3, .4))

fig2 <- plot_grid(fig2a, fig2b, nrow = 2)

pdf("/work-zfs/abattle4/parsana/networks_correction/publication_figures/fig2.pdf", height = 4.5, width = 7.2)
print(fig2)
dev.off()
#pdf("/work-zfs/abattle4/parsana/networks_correction/publication_figures/fig2.pdf", height = 4.5, width = 7.2)
#print(fig2)
#dev.off()

# source("/work-zfs/abattle4/parsana/networks_correction/src/config.R")
library(cowplot)

theme_set(theme_cowplot(font_size=9)) # reduce default font size
## categories to plot
#cat.plot <- c("uncorrected", "RIN", "PC")

# select category to plot
cutheights <- seq(0.9,1.0, length.out = 50)
lambda <- seq(0.3,1.0, length.out = 50)

cat.plot <- c("uncorrected", "RIN", "multi-covariate", "PC")
# select category to plot
select_category <- function(category_name, pr_table){
pr_table <- pr_table[which(pr_table$type %in% category_name),]
pr_table$type <- factor(pr_table$type, levels = category_name)
pr_table$cutheights <- rep(cutheights,length(category_name))
pr_table
}

plot.thyroid <- readRDS("/work-zfs/abattle4/parsana/networks_correction/results/PR/pr_density_wgcna-signed_canonical_thyroid.Rds")
plot.thyroid <- select_category(cat.plot, plot.thyroid)
plot.thyroid <- ggplot(plot.thyroid, aes(x = cutheights, y = density, colour = type)) + geom_point(size = 0.3) +
xlab("cut-heights") + ylab("# of edges")+ggtitle("Thyroid")

plot.lung <- readRDS("/work-zfs/abattle4/parsana/networks_correction/results/PR/pr_density_wgcna-signed_canonical_lung.Rds")
plot.lung <- select_category(cat.plot, plot.lung)
plot.lung <- ggplot(plot.lung, aes(x = cutheights, y = density, colour = type)) + geom_point(size = 0.3) +
xlab("cut-heights") + ylab("# of edges")+ggtitle("Lung")

plot.blood <- readRDS("/work-zfs/abattle4/parsana/networks_correction/results/PR/pr_density_wgcna-signed_canonical_blood.Rds")
plot.blood <- select_category(cat.plot, plot.blood)
plot.blood <- ggplot(plot.blood, aes(x = cutheights, y = density, colour = type)) + geom_point(size = 0.3) +
xlab("cut-heights") + ylab("# of edges")+ggtitle("Whole Blood")


fig4.wgcna <- plot_grid(plot.blood + xlim(1.0,0.9) + theme(legend.position="none"),
plot.lung + xlim(1.0,0.9) + theme(legend.position="none"),
plot.thyroid + xlim(1.0,0.9) + theme(legend.position="none"),
align = 'vh',
labels = c("g", "h", "i"),
hjust = -1,
nrow = 1
)
legend.wgcna<- get_legend(plot.lung +
theme(legend.key = element_rect(color = "black", linetype = "solid", size = 0.5),
legend.key.size = unit(0.3, "cm"), legend.key.height=unit(1,"line")) +
guides(colour = guide_legend(override.aes = list(size= 1)), fill=guide_legend("type")))

fig4.a <- plot_grid( fig4.wgcna, legend.wgcna, rel_widths = c(3, .4))

## Glasso
select_category <- function(category_name, pr_table){
pr_table <- pr_table[which(pr_table$type %in% category_name),]
pr_table$type <- factor(pr_table$type, levels = category_name)
pr_table$lambda <- rep(lambda,length(category_name))
pr_table
}


plot.thyroid <- readRDS("/work-zfs/abattle4/parsana/networks_correction/results/PR/pr_density_glasso_canonical_thyroid.Rds")
plot.thyroid <- select_category(cat.plot, plot.thyroid)
plot.thyroid <- ggplot(plot.thyroid, aes(x = lambda, y = density, colour = type)) + geom_point(size = 0.3) +
xlab("lambda") + ylab("# of edges")+ggtitle("Thyroid")

plot.lung <- readRDS("/work-zfs/abattle4/parsana/networks_correction/results/PR/pr_density_glasso_canonical_lung.Rds")
plot.lung <- select_category(cat.plot, plot.lung)
plot.lung <- ggplot(plot.lung, aes(x = lambda, y = density, colour = type)) + geom_point(size = 0.3) +
xlab("lambda") + ylab("# of edges")+ggtitle("Lung")

plot.blood <- readRDS("/work-zfs/abattle4/parsana/networks_correction/results/PR/pr_density_glasso_canonical_blood.Rds")
plot.blood <- select_category(cat.plot, plot.blood)
plot.blood <- ggplot(plot.blood, aes(x = lambda, y = density, colour = type)) + geom_point(size = 0.3) +
xlab("lambda") + ylab("# of edges")+ggtitle("Whole Blood")


fig4.glasso <- plot_grid(plot.blood + xlim(0.3,1.0) + theme(legend.position="none"),
plot.lung + xlim(0.3,1.0) + theme(legend.position="none"),
plot.thyroid + xlim(0.3,1.0) + theme(legend.position="none"),
align = 'vh',
labels = c("j", "k", "l"),
hjust = -1,
nrow = 1
)
legend.glasso <- get_legend(plot.lung +
theme(legend.key = element_rect(color = "black", linetype = "solid", size = 0.5),
legend.key.size = unit(0.3, "cm"), legend.key.height=unit(1,"line")) +
guides(colour = guide_legend(override.aes = list(size= 1)), fill=guide_legend("type")))

fig4.b <- plot_grid( fig4.glasso, legend.glasso, rel_widths = c(3, .4))

fig4 <- plot_grid(fig2a, fig2b, fig4.a, fig4.b, nrow = 4)

pdf("/work-zfs/abattle4/parsana/networks_correction/publication_figures/fig2.pdf", height = 9, width = 7.2)
print(fig4)
dev.off()

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