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Author: Wang-RJ

resample_alleleage/resample_alleleage.R

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+# analyze redrawn allele ages
+redraw_frames <- list()
+for(i in 25:34) {
+  redraw <- read.table(paste("Mutations/spectral/manuscript/submit/revisions/family_redraw/TGP_10kgacounts.redraw", i, sep = ""))
+  names(redraw) <- count_header
+  redraw <- cbind(redraw[,mut_classes] + redraw[,complementary_classes],
+                  CpG = redraw$CpG, bin_age = redraw$bin_age)
+  redraw_frames[[i-24]] <- make_plotframes(phasedstrictCT_model, redraw, TGPphased_boot10kga_ests)[[2]]
+}
+
+redraw_sexaves <- lapply(redraw_frames, "[", c("sexave"))
+
+redraw_sexaves <- mapply(cbind, redraw_sexaves,
+                         data.frame(bin_age = tgp_phased10kgaplots[[2]]$bin_age),
+                         SIMPLIFY = FALSE)
+
+redraw_ggframe <- do.call(rbind, mapply(cbind, redraw_sexaves,
+                                        lapply(1:10, function(i) {
+                                          data.frame(redraw_idx = rep(i, 100)) }),
+                                        SIMPLIFY = FALSE))
+names(redraw_ggframe)[2] <- "bin_age"
+
+ggplot(redraw_ggframe, aes(y = sexave, x = bin_age, col = factor(redraw_idx))) +
+  geom_smooth(method = "loess", se = FALSE, span = 0.65) +
+  geom_smooth(data = tgp_phased10kgaplots[[2]], aes(y = sexave, x = bin_age, col = 'mean'), lwd = 1, lty = 3,
+              formula = y ~ x, method = "loess", span = 0.65, se = FALSE, color = 'black') +
+  geom_ribbon(data = tgp_phased10kgaplots[[2]], aes(x = bin_age, y = sexave, col = 'mean',
+                                                    ymin = sexave_lower, ymax = sexave_upper),
+              alpha = 0.15, color = NA) +
+  coord_cartesian(ylim = c(13.5,38.5)) + #scale_color_manual(values = rev(pal_aaas("default")(2))) +
+  axis_formatting + annotation_logticks(sides = "b") +
+  scale_x_log10(minor_breaks = c(1:9 * 100, 1:9 * 1000)) + 
+  labs(y = "generation interval (years)", x = "allele age (generations ago)") +
+  theme(legend.position = "none")