Simulation analysis for all lines
Yuanhua Huang & Davis J. McCarthy
Last updated: 2018-08-24
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Load libraries and simulation results
library(ggpubr)
library(tidyverse)
library(cardelino)
library(viridis)
library(cowplot)
lines <- c("euts", "fawm", "feec", "fikt", "garx", "gesg", "heja", "hipn",
"ieki", "joxm", "kuco", "laey", "lexy", "naju", "nusw", "oaaz",
"oilg", "pipw", "puie", "qayj", "qolg", "qonc", "rozh", "sehl",
"ualf", "vass", "vuna", "wahn", "wetu", "xugn", "zoxy", "vils")Load simulation results
all_files <- paste0(lines, ".simulate.rds")
assign_0 <- matrix(0, nrow = 500, ncol = length(lines))
assign_1 <- matrix(0, nrow = 500, ncol = length(lines))
prob_all <- matrix(0, nrow = 500, ncol = length(lines))
for (i in seq_len(length(all_files))) {
afile <- all_files[i]
sim_dat <- readRDS(file.path("data", "simulations", afile))
assign_0[, i] <- get_prob_label(sim_dat$I_sim)
assign_1[, i] <- get_prob_label(sim_dat$prob_Gibbs)
prob_all[, i] <- get_prob_value(sim_dat$prob_Gibbs, mode = "best")
}Load results from real data
all_files <- paste0("cardelino_results.", lines,
".filt_lenient.cell_coverage_sites.rds")
n_sites <- rep(0, length(lines))
n_clone <- rep(0, length(lines))
recall_all <- rep(0, length(lines))
for (i in seq_len(length(all_files))) {
afile <- all_files[i]
carde_dat <- readRDS(file.path("data", "cell_assignment", afile))
n_sites[i] <- nrow(carde_dat$D)
n_clone[i] <- ncol(carde_dat$prob_mat)
recall_all[i] <- mean(get_prob_value(carde_dat$prob_mat, mode = "best") > 0.5)
}Overall correlation in assignment rates (recall) from simulated and observed data is 0.959.
precision_simu <- rep(0, length(lines))
for (i in seq_len(length(lines))) {
idx <- prob_all[, i] > 0.5
precision_simu[i] <- mean(assign_0[idx, i] == assign_1[idx, i])
}
df <- data.frame(line = lines, n_sites = n_sites, n_clone = n_clone,
recall_real = recall_all, recall_simu = colMeans(prob_all > 0.5),
precision_simu = precision_simu)Plot observed vs simulated assignment rates (recall)
df %>%
dplyr::mutate(sites_per_clone = cut(n_sites / pmax(n_clone - 1, 1),
breaks = c(0, 3, 8, 15, 25, 60))) %>%
ggplot(
aes(x = recall_simu, y = recall_real,
fill = sites_per_clone)) +
geom_abline(slope = 1, intercept = 0, colour = "gray40", linetype = 2) +
geom_smooth(aes(group = 1), method = "lm", colour = "firebrick") +
geom_point(size = 3, shape = 21) +
xlim(0, 1) + ylim(0, 1) +
scale_fill_manual(name = "mean\n# variants\nper clonal\nbranch",
values = magma(6)[-1]) +
guides(colour = FALSE, group = FALSE) +
xlab("Assignment rate: simulated") +
ylab("Assignment rate: observed")
ggsave("figures/simulations/assign_rate_obs_v_sim.png",
height = 4.5, width = 5)
ggsave("figures/simulations/assign_rate_obs_v_sim.pdf",
height = 4.5, width = 5)Plot simulation precision-recall curve
df %>%
dplyr::mutate(sites_per_clone = cut(n_sites / n_clone,
breaks = c(0, 5, 10, 20, 40))) %>%
ggplot(
aes(x = recall_simu, y = precision_simu,
fill = sites_per_clone)) +
geom_hline(yintercept = 0.85, colour = "gray40", linetype = 2) +
geom_smooth(aes(group = 1), method = "lm", colour = "firebrick") +
geom_point(size = 3, shape = 21) +
xlim(0, 1) + ylim(0, 1) +
scale_fill_manual(name = "mean\n# variants\nper clone",
values = magma(5)[-1]) +
guides(colour = FALSE, group = FALSE) +
xlab("Assignment rate (recall)") +
ylab("Precision")
ggsave("figures/simulations/sim_precision_v_recall.png",
height = 4.5, width = 5.5)
ggsave("figures/simulations/sim_precision_v_recall.pdf",
height = 4.5, width = 5.5)Clone statistics
Table showing the number of lines with 2, 3 and 4 clones.
table(df$n_clone)
2 3 4
4 24 4 Summary of the average number of mutations per clonal branch across lines.
summary(df$n_sites / (df$n_clone - 1)) Min. 1st Qu. Median Mean 3rd Qu. Max.
3.00 8.50 11.50 18.69 25.00 57.50 Session information
devtools::session_info()Session info ------------------------------------------------------------- setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_GB.UTF-8
tz Europe/London
date 2018-08-24 Packages ----------------------------------------------------------------- package * version date source
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