cashr
Last updated: 2018-10-06
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Generate the inflated vs in-between vs deflated noise figure in the paper.
library(ggplot2)
FDP.list <- readRDS("../output/paper/simulation/FDP.list.rds")
TDP.list <- readRDS("../output/paper/simulation/TDP.list.rds")
z.list <- readRDS("../output/paper/simulation/z.list.rds")
pi0.list <- readRDS("../output/paper/simulation/pi0.list.rds")
pi0.vec <- c(0.5, 0.9, 0.99)
q.vec <- seq(0.001, 0.20, by = 0.001)
q <- 0.1
method.name.FDR <- c("cashr", "BH", "qvalue", "ashr", "locfdr")
method.col.FDR <- scales::hue_pal()(length(method.name.FDR))[c(5, 1, 2, 4, 3)]
#####################################
boxplot.quantile <- function(x) {
r <- quantile(x, probs = c(0.10, 0.25, 0.5, 0.75, 0.90))
names(r) <- c("ymin", "lower", "middle", "upper", "ymax")
return(r)
}
boxplot.quantile.sq <- function (x) {
r <- sqrt(quantile(x^2, probs = c(0.10, 0.25, 0.5, 0.75, 0.90)))
names(r) <- c("ymin", "lower", "middle", "upper", "ymax")
return(r)
}
mean.sq <- function (x) {
r <- sqrt(mean(x^2))
return(r)
}
mysqrt_trans <- function() {
scales::trans_new("mysqrt",
transform = base::sqrt,
inverse = function(x) ifelse(x<0, 0, x^2),
domain = c(0, Inf))
}
###############################
sd.z <- sapply(z.list, sd)
Noise <- cut(sd.z, breaks = c(0, quantile(sd.z, probs = 1 : 2 / 3), Inf), labels = c("Deflated Noise", "In-between", "Inflated Noise"))
###############################
pi0.0.9 <- which(pi0.list == 0.9)
sd.z.0.9 <- sd.z[pi0.0.9]
typical.noise <- pi0.0.9[order(sd.z.0.9)[floor(quantile(seq(sd.z.0.9), c(0.1, 0.5, 0.9)))]]
z.list.sel <- z.list[typical.noise]
names(z.list.sel) <- c("Deflated Noise", "In-between", "Inflated Noise")
z.sep.ggdata <- reshape2::melt(z.list.sel, value.name = "z")
z.sep.plot <- ggplot(data = z.sep.ggdata, aes(x = z)) +
geom_histogram(aes(y = ..density..), binwidth = 0.2) +
facet_wrap(~L1, nrow = 1) +
stat_function(fun = dnorm, aes(color = "N(0, 1)"), lwd = 1.5, show.legend = TRUE) +
scale_color_manual(values = "blue") +
theme(axis.title.x = element_text(size = 15),
axis.text.x = element_text(size = 10),
axis.title.y = element_text(size = 15),
axis.text.y = element_text(size = 10),
strip.text = element_text(size = 15),
# strip.text = element_blank(),
legend.position = "left",
legend.title = element_blank(),
legend.text = element_text(size = 12),
legend.key = element_blank()
)
#########################################
FDP.q <- FDP.list[[which(q.vec == q)]]
FDP.q.noise.mat <- rbind.data.frame(
cbind.data.frame(Noise = rep("All", length(Noise)),
pi0 = factor(do.call(rbind, pi0.list)),
FDP.q),
cbind.data.frame(Noise,
pi0 = factor(do.call(rbind, pi0.list)),
FDP.q)
)
FDP.q.ggdata <- reshape2::melt(FDP.q.noise.mat, id.vars = c("Noise", "pi0"), variable.name = "Method", value.name = "FDP")
FDP.q.ggdata$Method <- factor(FDP.q.ggdata$Method, levels = c("CASH", "BHq", "qvalue", "ASH", "locfdr"))
FDP.q.ggdata$Method <- plyr::mapvalues(FDP.q.ggdata$Method, from = c("CASH", "BHq", "qvalue", "ASH", "locfdr"), to = c("cashr", "BH", "qvalue", "ashr", "locfdr"))
FDP.q.ggdata.0.9 <- FDP.q.ggdata[FDP.q.ggdata$pi0 == 0.9, ]
################################################
TDP.q <- TDP.list[[which(q.vec == q)]]
TDP.q.noise.mat <- rbind.data.frame(
cbind.data.frame(Noise = rep("All", length(Noise)),
pi0 = factor(do.call(rbind, pi0.list)),
TDP.q),
cbind.data.frame(Noise,
pi0 = factor(do.call(rbind, pi0.list)),
TDP.q)
)
TDP.q.ggdata <- reshape2::melt(TDP.q.noise.mat, id.vars = c("Noise", "pi0"), variable.name = "Method", value.name = "TDP")
TDP.q.ggdata$Method <- factor(TDP.q.ggdata$Method, levels = c("CASH", "BHq", "qvalue", "ASH", "locfdr"))
TDP.q.ggdata$Method <- plyr::mapvalues(TDP.q.ggdata$Method, from = c("CASH", "BHq", "qvalue", "ASH", "locfdr"), to = c("cashr", "BH", "qvalue", "ashr", "locfdr"))
TDP.q.ggdata.0.9 <- TDP.q.ggdata[TDP.q.ggdata$pi0 == 0.9, ]
##############################################################
# FDP.q.all.sep.plot <- ggplot(data = FDP.q.ggdata, aes(x = pi0, y = FDP, fill = Method, color = Method)) +
# stat_summary(fun.data = boxplot.quantile, geom = "boxplot", position = "dodge") +
# stat_summary(fun.y = mean, geom = "point", position = position_dodge(width = 0.9), show.legend = TRUE) +
# scale_color_manual(labels = method.name.FDR, values = method.col.FDR) +
# scale_fill_manual(labels = method.name.FDR, values = alpha(method.col.FDR, 0.35)) +
# facet_wrap(~Noise, nrow = 1) +
# geom_hline(yintercept = q, col = "black", linetype = "dashed", size = 1) +
# labs(x = expression(pi[0]), y = "FDP", title = bquote(paste("Nominal FDR = ", .(q)))) +
# theme(plot.title = element_text(size = 12, hjust = 0),
# axis.title.x = element_text(size = 15),
# axis.text.x = element_text(size = 10),
# axis.title.y = element_text(size = 15),
# axis.text.y = element_text(size = 10),
# strip.text = element_text(size = 15),
# legend.position = "bottom",
# legend.background = element_rect(color = "grey"),
# legend.text = element_text(size = 12)
# )
FDP.q.all.sep.plot <- ggplot(data = FDP.q.ggdata.0.9, aes(x = Method, y = FDP, fill = Method, color = Method)) +
stat_summary(fun.data = boxplot.quantile, geom = "boxplot", aes(width = 0.5), position = position_dodge(), show.legend = FALSE) +
stat_summary(fun.y = mean, geom = "point", position = position_dodge(width = 0.9), show.legend = FALSE) +
scale_x_discrete(limits = rev(levels(FDP.q.ggdata.0.9$Method))) +
coord_flip() +
scale_color_manual(labels = method.name.FDR, values = method.col.FDR) +
scale_fill_manual(labels = method.name.FDR, values = alpha(method.col.FDR, 0.35)) +
facet_wrap(~Noise, nrow = 1) +
geom_hline(yintercept = q, col = "black", linetype = "dashed", size = 1) +
labs(y = "FDP", title = bquote(paste("Nominal FDR = ", .(q), " (", g[1], " is Gaussian; ", pi[0] == 0.9, ")"))) +
expand_limits(y = 0) +
theme(plot.title = element_text(size = 12, hjust = 0),
axis.title.y = element_blank(),
axis.text.y = element_text(size = 15),
axis.title.x = element_text(size = 15),
axis.text.x = element_text(size = 10),
strip.text = element_text(size = 15),
legend.position = "bottom",
legend.background = element_rect(color = "grey"),
legend.text = element_text(size = 12)
)
Warning: Ignoring unknown aesthetics: width
FDP.sqrt.q.all.sep.plot <- ggplot(data = FDP.q.ggdata.0.9, aes(x = Method, y = FDP, fill = Method, color = Method)) +
stat_summary(fun.data = boxplot.quantile.sq, geom = "boxplot", aes(width = 0.5), position = position_dodge(), show.legend = FALSE) +
stat_summary(fun.y = mean.sq, geom = "point", position = position_dodge(width = 0.9), show.legend = FALSE) +
scale_x_discrete(limits = rev(levels(FDP.q.ggdata.0.9$Method))) +
scale_y_continuous(trans = "mysqrt", breaks = c(0, 0.1, 0.2, 0.4, 0.6, 0.8)) +
coord_flip() +
scale_color_manual(labels = method.name.FDR, values = method.col.FDR) +
scale_fill_manual(labels = method.name.FDR, values = alpha(method.col.FDR, 0.35)) +
facet_wrap(~Noise, nrow = 1) +
geom_hline(yintercept = q, col = "black", linetype = "dashed", size = 1) +
labs(x = expression(pi[0]), y = "FDP", title = bquote(paste("Nominal FDR = ", .(q), " (", g[1], " is Gaussian; ", pi[0] == 0.9, ")"))) +
expand_limits(y = 0) +
theme(plot.title = element_text(size = 12, hjust = 0),
axis.title.y = element_blank(),
axis.text.y = element_text(size = 15),
axis.title.x = element_text(size = 15),
axis.text.x = element_text(size = 10),
strip.text = element_text(size = 15),
legend.position = "bottom",
legend.background = element_rect(color = "grey"),
legend.text = element_text(size = 12)
)
Warning: Ignoring unknown aesthetics: width
###############################################
blank.ggdata <- data.frame()
blank.plot <- ggplot(data = blank.ggdata) +
theme(panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
plot.background = element_blank()) +
geom_blank()
z.sep.plot.save <- gridExtra::arrangeGrob(blank.plot, z.sep.plot, nrow = 1, widths = c(0.55, 3.5))
FDP.q.sep.plot.save <- gridExtra::arrangeGrob(z.sep.plot.save, FDP.q.all.sep.plot, heights = c(1, 1.2))
FDP.sqrt.q.sep.plot.save <- gridExtra::arrangeGrob(z.sep.plot.save, FDP.sqrt.q.all.sep.plot, heights = c(1, 1.2))
ggsave("../output/paper/FDP.q.sep.pdf", FDP.q.sep.plot.save, height = 4.5, width = 10)
ggsave("../output/paper/FDP.sqrt.q.sep.pdf", FDP.sqrt.q.sep.plot.save, height = 4.5, width = 10)
##############################################
TDP.q.all.sep.plot <- ggplot(data = TDP.q.ggdata.0.9, aes(x = Method, y = TDP, fill = Method, color = Method)) +
stat_summary(fun.data = boxplot.quantile, geom = "boxplot", aes(width = 0.5), position = position_dodge(), show.legend = FALSE) +
coord_flip() +
stat_summary(fun.y = mean, geom = "point", position = position_dodge(width = 0.9), show.legend = FALSE) +
scale_x_discrete(limits = rev(levels(FDP.q.ggdata.0.9$Method))) +
scale_color_manual(labels = method.name.FDR, values = method.col.FDR) +
scale_fill_manual(labels = method.name.FDR, values = alpha(method.col.FDR, 0.35)) +
facet_wrap(~Noise, nrow = 1) +
labs(x = expression(pi[0]), y = "TDP") +
expand_limits(y = 0) +
theme(axis.title.y = element_blank(),
axis.text.y = element_text(size = 15),
axis.title.x = element_text(size = 15),
axis.text.x = element_text(size = 10),
strip.text = element_text(size = 15),
legend.position = "bottom",
legend.background = element_rect(color = "grey"),
legend.text = element_text(size = 12)
)
Warning: Ignoring unknown aesthetics: width
FDP.TDP.q.sep.plot.save <- gridExtra::arrangeGrob(z.sep.plot.save, FDP.q.all.sep.plot + theme(plot.title = element_text(size = 15, hjust = 0)), TDP.q.all.sep.plot, heights = c(1, 1.2, 1.1))
FDP.sqrt.TDP.q.sep.plot.save <- gridExtra::arrangeGrob(z.sep.plot.save, FDP.sqrt.q.all.sep.plot + theme(plot.title = element_text(size = 15, hjust = 0)), TDP.q.all.sep.plot, heights = c(1, 1.2, 1.1))
ggsave("../output/paper/FDP.TDP.q.sep.pdf", FDP.TDP.q.sep.plot.save, height = 6.5, width = 10)
ggsave("../output/paper/FDP.sqrt.TDP.q.sep.pdf", FDP.sqrt.TDP.q.sep.plot.save, height = 6.5, width = 10)
sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_2.2.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 knitr_1.20 whisker_0.3-2
[4] magrittr_1.5 workflowr_1.1.1 munsell_0.4.3
[7] colorspace_1.3-2 rlang_0.1.6 stringr_1.3.0
[10] plyr_1.8.4 tools_3.4.3 grid_3.4.3
[13] gtable_0.2.0 R.oo_1.22.0 git2r_0.21.0
[16] htmltools_0.3.6 yaml_2.1.18 lazyeval_0.2.1
[19] rprojroot_1.3-2 digest_0.6.15 tibble_1.4.2
[22] gridExtra_2.3 reshape2_1.4.3 R.utils_2.7.0
[25] evaluate_0.10.1 rmarkdown_1.9 labeling_0.3
[28] stringi_1.1.6 pillar_1.1.0 compiler_3.4.3
[31] scales_0.5.0 backports_1.1.2 R.methodsS3_1.7.1
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