Last updated: 2018-12-14

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Unstaged changes:
    Modified:   analysis/cash_plots_2.rmd
    Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
Expand here to see past versions:
    File Version Author Date Message
    rmd 4fe64f2 Lei Sun 2018-12-05 plots
    rmd 3638fea LSun 2018-11-29 shoulder figs
    rmd b3c8961 Lei Sun 2018-11-28 shoulder
    rmd 5d335c5 LSun 2018-11-28 shoulder figs
    rmd c87b8d2 Lei Sun 2018-11-11 figures 
z.sel <- readRDS("../output/paper/simulation/z.sel.rds")
z <- z.sel[3, ]
p <- pnorm(-abs(z)) * 2
# setEPS()
# postscript("../output/paper/hist_z.eps", width = 5, height = 5)
pdf("../output/paper/hist_z.pdf", width = 6.5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

hist(z, breaks = seq(-10, 10, by = 0.1), prob = TRUE, ylim = c(0, dnorm(0)), xlab = "z-score", xlim = range(c(abs(z), -abs(z))), main = expression("(a): Histogram of correlated z-scores"), cex.main = 2, cex.lab = 2)

x.plot = seq(- max(abs(z.sel)) - 2, max(abs(z.sel)) + 2, length = 1000)
lines(x.plot, dnorm(x.plot), col = "blue", lwd = 3)

legend("topright", expression('N(0,1)'), lty = 1, col = 'blue', lwd = 3, cex = 1.75, bty = 'n', seg.len = 1.5, x.intersp = 0.5)

dev.off()
quartz_off_screen 
                2 
# setEPS()
# postscript("../output/paper/pval_z.eps", width = 5, height = 5)
pdf("../output/paper/pval_z.pdf", width = 6.5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

hist(p, prob = TRUE, breaks = seq(0, 1, by = 0.01), xlab = "p-value", main = expression("(b): Histogram of correlated p-values"), cex.main = 2, cex.lab = 2)

segments(x0 = 0, x1 = 1, y0 = 1, y1 = 1, col = "blue", lwd = 3)

legend("topright", expression('Uniform[0,1]'), lty = 1, col = 'blue', lwd = 3, cex = 1.75, bty = 'n', seg.len = 1.5, x.intersp = 0.5)

dev.off()
quartz_off_screen 
                2 
thresh.color <- c("maroon", "purple", "orange")
#thresh.color <- scales::hue_pal()(10)[5 : 7]

set.seed(5)
p.norm.1 <- pnorm(-abs(rnorm(1e4))) * 2
set.seed(25)
p.norm.1.6 <- pnorm(-abs(rnorm(1e4, 0, 1.6))) * 2
y.max <- -log(min(p.norm.1, p, p.norm.1.6))
y.max <- 20
# setEPS()
# postscript("../output/paper/ecdf_z.eps", width = 5, height = 5)
pdf("../output/paper/ecdf_z.pdf", width = 5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

plot(ecdf(z), xlab = "z-score", ylab = "CDF", lwd = 2, main = expression("(c): Empirical CDF"), cex.main = 2, cex.lab = 2, xlim = c(-max(abs(z)), max(abs(z))))
lines(seq(-6, 6, by = 0.01), pnorm(seq(-6, 6, by = 0.01)), col = "blue", lwd = 3, lty = 2)
lines(seq(-6, 6, by = 0.01), pnorm(seq(-6, 6, by = 0.01), 0, 1.6), col = "green", lwd = 3, lty = 4)
rect(xleft = c(-5, 2.5),
     xright = c(-2.5, 5),
     ytop = c(0.05, 1),
     ybottom = c(0, 0.95), border = "red", lty = c(1, 5))
legend("topleft", c("Correlated z-scores", expression(N(0,1)), expression(N(0, 1.6^2))), lty = c(1, 2, 4), col = c("black", "blue", "green"), lwd = 3, cex = 1.25, bty = 'n', seg.len = 1.5, x.intersp = 0.5)

dev.off()
quartz_off_screen 
                2 
# setEPS()
# postscript("../output/paper/ecdf_z_left.eps", width = 5, height = 5)
pdf("../output/paper/ecdf_z_left.pdf", width = 5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

plot(ecdf(z), xlab = "z-score", ylab = "CDF", main = expression("(d): Left Tail of CDF"), lwd = 3, xlim = c(-5, -2.5), ylim = c(0, 0.05), cex.main = 2, cex.lab = 2, bty = "n")
box(col = "red")
lines(seq(-6, 6, by = 0.01), pnorm(seq(-6, 6, by = 0.01)), col = "blue", lwd = 3, lty = 2)
lines(seq(-6, 6, by = 0.01), pnorm(seq(-6, 6, by = 0.01), 0, 1.6), col = "green", lwd = 3, lty = 4)

legend("topleft", c("Correlated z-scores", expression(N(0,1)), expression(N(0, 1.6^2))), lty = c(1, 2, 4), col = c("black", "blue", "green"), lwd = 3, cex = 1.25, bty = 'n', seg.len = 1.5, x.intersp = 0.5)

dev.off()
quartz_off_screen 
                2 
# setEPS()
# postscript("../output/paper/ecdf_z_right.eps", width = 5, height = 5)
pdf("../output/paper/ecdf_z_right.pdf", width = 5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

plot(ecdf(z), xlab = "z-score", ylab = "CDF", main = expression("(e): Right Tail of CDF"), lwd = 3, xlim = c(2.5, 5), ylim = c(0.95, 1), cex.main = 2, cex.lab = 2, bty = "n")
box(col = "red", lty = 5)
lines(seq(-6, 6, by = 0.01), pnorm(seq(-6, 6, by = 0.01)), col = "blue", lwd = 3, lty = 2)
lines(seq(-6, 6, by = 0.01), pnorm(seq(-6, 6, by = 0.01), 0, 1.6), col = "green", lwd = 3, lty = 4)

legend("bottomright", c("Correlated z-scores", expression(N(0,1)), expression(N(0, 1.6^2))), lty = c(1, 2, 4), col = c("black", "blue", "green"), lwd = 3, cex = 1.25, bty = 'n', seg.len = 1.5, x.intersp = 0.5)

dev.off()
quartz_off_screen 
                2 
# setEPS()
# postscript("../output/paper/pval_log_z.eps", width = 5, height = 5)
pdf("../output/paper/pval_log_z.pdf", width = 5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

plot(sample(-log(p)), ylim = c(0, y.max), ylab = "-log(p-value)", main = expression('(f): Correlated z-scores'), cex.main = 2, cex.lab = 2, pch = 19)
abline(h = -log(c(
  0.005,
  pnorm(-sqrt(2 * log(1e4))) * 2,
  0.05 / 1e4
)), lwd = 3, col = thresh.color, lty = c(1, 2, 4))

dev.off()
quartz_off_screen 
                2 
# setEPS()
# postscript("../output/paper/pval_log_N01.eps", width = 5, height = 5)
pdf("../output/paper/pval_log_N01.pdf", width = 5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

plot(-log(p.norm.1), ylim = c(0, y.max), ylab = "-log(p-value)", main = expression("(g): iid N(0,1) z-scores"), col = "blue", cex.main = 2, cex.lab = 2, pch = 19)
abline(h = -log(c(
  0.005,
  pnorm(-sqrt(2 * log(1e4))) * 2,
  0.05 / 1e4
)), lwd = 3, col = thresh.color, lty = c(1, 2, 4))

legend("top",
       legend = c(
         latex2exp::TeX('p-value$= 0.05 / 10^4$'),
         'Univsal Threshold',
         latex2exp::TeX('p-value$= 0.005')
         ), lty = c(4, 2, 1), lwd = 3, xpd = NA,
       col = thresh.color[3 : 1], ncol = 1, bty = 'n', cex = 1.25)

dev.off()
quartz_off_screen 
                2 
# setEPS()
# postscript("../output/paper/pval_log_N01.6.eps", width = 5, height = 5)
pdf("../output/paper/pval_log_N016.pdf", width = 5, height = 5)

par(mar = c(4.5, 4.5, 2.5, 1))

plot(-log(p.norm.1.6), ylim = c(0, y.max), ylab = "-log(p-value)", main = expression(paste("(h): iid ", N(0, 1.6^2), " z-scores")), col = "green", cex.main = 2, cex.lab = 2, pch = 19)
abline(h = -log(c(
  0.005,
  pnorm(-sqrt(2 * log(1e4))) * 2,
  0.05 / 1e4
)), lwd = 3, col = thresh.color, lty = c(1, 2, 4))

# legend("topright", inset = c(-0.52, 0.3),
#        legend = c(
#          latex2exp::TeX('$p = 0.05 / 10^4$'),
#          'Univ Thresh',
#          "p = 0.005"
#          ), lty = c(4, 2, 1), lwd = 3, xpd = NA,
#        col = thresh.color[3 : 1], ncol = 1, cex = 1.5, bty = "n", x.intersp = 0.5, seg.len = 1.5)

dev.off()
quartz_off_screen 
                2

Session information

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

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     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.16      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.2.2     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.6.0     latex2exp_0.4.0   rmarkdown_1.9    
[16] tools_3.4.3       stringr_1.3.1     yaml_2.1.19      
[19] compiler_3.4.3    htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1