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study05_broad_analysis.R
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# Create a function that is able to parse a matrix containing alot of data
# -----------------------------------------------------------------------------
# Set up directories
if (!exists("git.dir")) {
rm(list = ls(all = T))
wd <- c("C:/Users/Jim Hughes/Documents", "C:/Users/hugjh001/Documents",
"C:/Users/hugjh001/Desktop", "C:/windows/system32")
graphics.off()
if (getwd() == wd[1]) {
gir.dir <- paste0(getwd(), "/GitRepos")
reponame <- "optinterval"
} else if (getwd() == wd[2]) {
git.dir <- getwd()
reponame <- "optinterval"
} else if (getwd() == wd[3] | getwd() == wd[4]) {
git.dir <- "E:/Hughes/Git"
reponame <- "splines"
}
rm("wd")
}
# Load packages
#library(GA)
library(ggplot2)
theme_bw2 <- theme_set(theme_bw(base_size = 14))
theme_update(plot.title = element_text(hjust = 0.5))
library(plyr)
library(grid)
# Source scripts and r objects to set up environment
source(paste(git.dir, reponame, "study_functions.R", sep = "/"))
source(paste(git.dir, reponame, "sumstat_functions.R", sep = "/"))
# Source data
d2b <- readRDS(paste(git.dir, reponame, "d2b-broad.rds", sep = "/"))
d3b <- readRDS(paste(git.dir, reponame, "d3b-broad.rds", sep = "/"))
d1a <- readRDS(paste(git.dir, reponame, "d1a-broad.rds", sep = "/"))
d2a <- readRDS(paste(git.dir, reponame, "d2a-broad.rds", sep = "/"))
d3a <- readRDS(paste(git.dir, reponame, "d3a-broad.rds", sep = "/"))
# -----------------------------------------------------------------------------
# Data structure
# d2b[[1]], d3b[[2]], d1a[[3]], d2a[[4]], d3a[[5]]
# names(d[[#]]) -> "data" "result"
# names(d[[#]]$result) -> "auc" "cmax" "tmax"
data.names <- c("d2b", "d3b", "d1a", "d2a", "d3a")
slot.names <- c("auc", "cmax", "tmax")
res <- data.frame(NULL)
plotdata <- data.frame(NULL)
for (i in 1:5) {
r.out <- data.frame(NULL)
d.out <- data.frame(NULL)
for (j in 1:3) {
d.in <- get(data.names[i])[[i]]$result[slot.names[j]]
d.melt <- data.frame(
data = data.names[i],
metric = slot.names[j],
ref = rep(d.in[[1]]$true, 3),
test = c(d.in[[1]]$basic,
d.in[[1]]$optint,
d.in[[1]]$optintwCmax),
type = c(rep("bas", 1000), rep("opt", 1000), rep("optc", 1000)))
d.melt$prop <- with(d.melt, test/ref)
d.out <- rbind(d.out, d.melt)
r.out <- rbind(r.out, ddply(d.melt, .(type), function(x) {
c(data = data.names[i], metric = slot.names[j], sumfuncBOX(x$prop))
}))
}
res <- rbind(res, r.out)
plotdata <- rbind(plotdata, d.out)
}
# -----------------------------------------------------------------------------
box.plot.fn <- function(metric, data, x, zoom, layout = NULL) {
subplot <- plotdata[plotdata$metric == metric & plotdata$data == data, ]
subplot$type <- as.factor(subplot$type)
levels(subplot$type) <- c("Basic", "Optint", "Optint w/ Cmax")
plotobj <- ggplot(subplot, aes(x = type, y = prop))
plotobj <- plotobj + geom_hline(yintercept = c(0.8, 1.25), color = "green4", linetype = "dashed")
plotobj <- plotobj + geom_boxplot()
plotobj <- plotobj + ggtitle(paste("Data:", data, "- Metric:", metric))
plotobj <- plotobj + xlab("\nMethod")
plotobj <- plotobj + ylab("Method/Reference Ratio\n")
if (zoom) {
# ylim.box <- boxplot.stats(subplot$prop)$stats[c(1, 5)]
ylim.box <- c(0.6, 1.7) # "broad_boxplot_auc_zoom.png"
plotobj <- plotobj + coord_cartesian(ylim = ylim.box)
}
if (x) plotobj <- plotobj + stat_summary(fun.y = mean, geom = "point", shape = 4, size = 4)
if (is.null(layout)) print(plotobj)
else print(plotobj, vp = layout)
}
forest.plot.fn <- function(metric, data, layout = NULL) {
subplot <- res[res$metric == metric & res$data == data, ]
subplot$type <- factor(subplot$type, levels = rev(subplot$type))
levels(subplot$type) <- c("Optint w/ Cmax", "Optint", "Basic")
subplot$median <- as.numeric(subplot$median)
subplot$q025 <- as.numeric(subplot$q025)
subplot$q25 <- as.numeric(subplot$q25)
subplot$q75 <- as.numeric(subplot$q75)
subplot$q975 <- as.numeric(subplot$q975)
plotobj <- ggplot(subplot, aes(x = type, y = median))
plotobj <- plotobj + geom_linerange(aes(ymin = q025, ymax = q975), color = "red")
plotobj <- plotobj + geom_pointrange(aes(ymin = q25, ymax = q75))
plotobj <- plotobj + geom_hline(yintercept = 1, lty = 2, color = "green4")
plotobj <- plotobj + ggtitle(paste("Data:", data, "- Metric:", metric))
plotobj <- plotobj + xlab("\nMethod")
plotobj <- plotobj + scale_y_continuous("Method/Reference Ratio\n")
plotobj <- plotobj + coord_flip()
if (is.null(layout)) print(plotobj)
else print(plotobj, vp = layout)
}
# -----------------------------------------------------------------------------
# png("broad_boxplot_auc_zoom.png", width = 1200, height = 480)
# png("broad_boxplot_auc_nozoom.png", width = 1200, height = 480)
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,5)))
box.plot.fn("auc", "d1a", F, T, vplayout(1,1))
box.plot.fn("auc", "d2a", F, T, vplayout(1,2))
box.plot.fn("auc", "d3a", F, T, vplayout(1,3))
box.plot.fn("auc", "d2b", F, T, vplayout(1,4))
box.plot.fn("auc", "d3b", F, T, vplayout(1,5))
dev.off()
# png("broad_boxplot_cmax_nozoom.png", width = 720, height = 480)
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("cmax", "d1a", F, F, vplayout(1,1))
box.plot.fn("cmax", "d2a", F, F, vplayout(1,2))
box.plot.fn("cmax", "d3a", F, F, vplayout(1,3))
dev.off()
# png("broad_boxplot_tmax_nozoom.png", width = 720, height = 480)
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("tmax", "d1a", F, F, vplayout(1,1))
box.plot.fn("tmax", "d2a", F, F, vplayout(1,2))
box.plot.fn("tmax", "d3a", F, F, vplayout(1,3))
dev.off()
# -----------------------------------------------------------------------------
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("auc", "d1a", F, T, vplayout(1,1))
box.plot.fn("cmax", "d1a", F, T, vplayout(1,2))
box.plot.fn("tmax", "d1a", F, T, vplayout(1,3))
dev.off()
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(3, 1)))
forest.plot.fn("auc", "d1a", vplayout(1,1))
forest.plot.fn("cmax", "d1a", vplayout(2,1))
forest.plot.fn("tmax", "d1a", vplayout(3,1))
dev.off()
# -----------------------------------------------------------------------------
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("auc", "d2a", F, F, vplayout(1,1))
box.plot.fn("cmax", "d2a", F, F, vplayout(1,2))
box.plot.fn("tmax", "d2a", F, F, vplayout(1,3))
dev.off()
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(3, 1)))
forest.plot.fn("auc", "d2a", vplayout(1,1))
forest.plot.fn("cmax", "d2a", vplayout(2,1))
forest.plot.fn("tmax", "d2a", vplayout(3,1))
dev.off()
# -----------------------------------------------------------------------------
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("auc", "d3a", F, T, vplayout(1,1))
box.plot.fn("cmax", "d3a", F, T, vplayout(1,2))
box.plot.fn("tmax", "d3a", F, T, vplayout(1,3))
dev.off()
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(3, 1)))
forest.plot.fn("auc", "d3a", vplayout(1,1))
forest.plot.fn("cmax", "d3a", vplayout(2,1))
forest.plot.fn("tmax", "d3a", vplayout(3,1))
dev.off()
# -----------------------------------------------------------------------------
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("auc", "d2b", F, T, vplayout(1,1))
box.plot.fn("cmax", "d2b", F, T, vplayout(1,2))
box.plot.fn("tmax", "d2b", F, T, vplayout(1,3))
dev.off()
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(3, 1)))
forest.plot.fn("auc", "d2b", vplayout(1,1))
forest.plot.fn("cmax", "d2b", vplayout(2,1))
forest.plot.fn("tmax", "d2b", vplayout(3,1))
dev.off()
# -----------------------------------------------------------------------------
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1,3)))
box.plot.fn("auc", "d3b", F, T, vplayout(1,1))
box.plot.fn("cmax", "d3b", F, T, vplayout(1,2))
box.plot.fn("tmax", "d3b", F, T, vplayout(1,3))
dev.off()
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
grid.newpage()
pushViewport(viewport(layout = grid.layout(3, 1)))
forest.plot.fn("auc", "d2b", vplayout(1,1))
forest.plot.fn("cmax", "d2b", vplayout(2,1))
forest.plot.fn("tmax", "d2b", vplayout(3,1))
dev.off()