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<h1 class="title toc-ignore">Predicting cell times for individuals</h1>
<h4 class="author"><em>Joyce Hsiao</em></h4>
</div>
<div id="TOC">
<ul>
<li><a href="#pipeline">Pipeline</a></li>
<li><a href="#top-x-cyclical-genes">Top X cyclical genes</a></li>
<li><a href="#prediction-error">Prediction error</a></li>
<li><a href="#session-information">Session information</a></li>
</ul>
</div>
<!-- The file analysis/chunks.R contains chunks that define default settings
shared across the workflowr files. -->
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<p><strong>Last updated:</strong> 2018-07-18</p>
<!-- Insert the code version (Git commit SHA1) if Git repository exists and R
package git2r is installed -->
<p><strong>Code version:</strong> 91067ec</p>
<hr />
<div id="pipeline" class="section level2">
<h2>Pipeline</h2>
<ol style="list-style-type: decimal">
<li><p>Split data to validation samples and training samples.</p>
<ul>
<li>The split samples are saved as <code>data/ind_XX_withheld.rds</code> and <code>data/ind_XX_training.rds</code>.<br />
</li>
<li>The code used to generated teh split samples is saved in <code>code/working/makedata_supervised.R</code>.</li>
</ul></li>
<li><p>In the training sample, repeat the following 5 times. Each time, take samples from 4 individuals, fit trendfilter and identified the top X cyclical genes, and the compute the error in predicting cell time of the held-out individual, as a function of the top X cyclical genes.</p>
<ul>
<li><code>code/run_methods.R</code>: runs all methods, including supervised, unsupervised trendfilter, unsupervised bspline, unsupervised lowess, seurat) and compute prediction error margin.<br />
</li>
<li><code>code/working/job_run_methods.train.ind.R</code> calls <code>code/run_methods.R</code></li>
<li><code>code/working/job_run_methods.train.ind.sbatch</code> submits jobs one fold at a time.</li>
</ul></li>
<li><p>Based on the training sample results, select the top best X genes and fit to the validation sample. Compute and compare the methods’ performance on the validation sample.</p></li>
</ol>
<hr />
</div>
<div id="top-x-cyclical-genes" class="section level2">
<h2>Top X cyclical genes</h2>
<p>time based on fucci only</p>
<pre class="r"><code># observed data
library(gplots)
inds <- c("NA19098", "NA18511", "NA18870", "NA19101", "NA18855", "NA19160")
ngenes <- c(5, seq(10, 11040, 10))
for (j in 1:length(inds)) {
ind <- inds[j]
gene_names <- rownames(readRDS(paste0("../data/results/ind_",ind,"_data_training_cyclical_genes.fold.",
1,".rds")))
genes_list <- lapply(1:length(ngenes), function(i) {
ngene <- ngenes[i]
tmp <- do.call(cbind, lapply(1:5, function(fold) {
fl_name <- paste0("../data/results/ind_",ind,"_data_training_cyclical_genes.fold.",
fold,".rds")
df <- readRDS(fl_name)
top_list <- rownames(df)[order(df$pve,decreasing = T)[1:ngene]]
rownames(df) %in% top_list
}) )
rownames(tmp) <- gene_names
return(rownames(tmp)[rowSums(tmp)>=4])
})
names(genes_list) <- ngenes
saveRDS(genes_list,
file = paste0("../data/results/ind_",ind,"_results_topgenes.rds"))
}
ind_NA19098_topgenes <- readRDS("../data/results/ind_NA19098_results_topgenes.rds")
ind_NA18511_topgenes <- readRDS("../data/results/ind_NA18511_results_topgenes.rds")
ind_NA18870_topgenes <- readRDS("../data/results/ind_NA18870_results_topgenes.rds")
ind_NA19101_topgenes <- readRDS("../data/results/ind_NA19101_results_topgenes.rds")
ind_NA18855_topgenes <- readRDS("../data/results/ind_NA18855_results_topgenes.rds")
ind_NA19160_topgenes <- readRDS("../data/results/ind_NA19160_results_topgenes.rds")
topgenes_list <- list(ind_NA19098_topgenes, ind_NA18511_topgenes, ind_NA18870_topgenes,
ind_NA19101_topgenes, ind_NA18855_topgenes, ind_NA19160_topgenes)
library(dplyr)
topgenes_combined <- lapply(1:length(ind_NA19160_topgenes), function(i) {
ll <- lapply(topgenes_list, "[[", i)
ll <- unlist(ll)
tab <- table(ll)
names(tab)[which(tab>=4)]
})
names(topgenes_combined) <- names(ind_NA19160_topgenes)
saveRDS(topgenes_combined, file="../data/results/ind_results_topgenes.rds")</code></pre>
<p>time based on fucci and dapi only</p>
<pre class="r"><code># observed data
library(gplots)
inds <- c("NA19098", "NA18511", "NA18870", "NA19101", "NA18855", "NA19160")
ngenes <- c(5, seq(10, 11040, 10))
for (j in 1:length(inds)) {
ind <- inds[j]
gene_names <- rownames(readRDS(paste0("../data/results/triple_ind_",ind,
"_data_training_cyclical_genes.fold.",
1,".rds")))
genes_list <- lapply(1:length(ngenes), function(i) {
ngene <- ngenes[i]
tmp <- do.call(cbind, lapply(1:5, function(fold) {
fl_name <- paste0("../data/results/triple_ind_",ind,
"_data_training_cyclical_genes.fold.",
fold,".rds")
df <- readRDS(fl_name)
top_list <- rownames(df)[order(df$pve,decreasing = T)[1:ngene]]
rownames(df) %in% top_list
}) )
rownames(tmp) <- gene_names
return(rownames(tmp)[rowSums(tmp)>=4])
})
names(genes_list) <- ngenes
saveRDS(genes_list,
file = paste0("../data/results/ind_",ind,"_results_topgenes_triple.rds"))
}
ind_NA19098_topgenes <- readRDS("../data/results/ind_NA19098_results_topgenes_triple.rds")
ind_NA18511_topgenes <- readRDS("../data/results/ind_NA18511_results_topgenes_triple.rds")
ind_NA18870_topgenes <- readRDS("../data/results/ind_NA18870_results_topgenes_triple.rds")
ind_NA19101_topgenes <- readRDS("../data/results/ind_NA19101_results_topgenes_triple.rds")
ind_NA18855_topgenes <- readRDS("../data/results/ind_NA18855_results_topgenes_triple.rds")
ind_NA19160_topgenes <- readRDS("../data/results/ind_NA19160_results_topgenes_triple.rds")
topgenes_list <- list(ind_NA19098_topgenes, ind_NA18511_topgenes, ind_NA18870_topgenes,
ind_NA19101_topgenes, ind_NA18855_topgenes, ind_NA19160_topgenes)
library(dplyr)
topgenes_combined <- lapply(1:length(ind_NA19160_topgenes), function(i) {
ll <- lapply(topgenes_list, "[[", i)
ll <- unlist(ll)
tab <- table(ll)
names(tab)[which(tab>=4)]
})
names(topgenes_combined) <- names(ind_NA19160_topgenes)
saveRDS(topgenes_combined, file="../data/results/ind_results_topgenes_triple.rds")</code></pre>
<p>Compare number of genes selected at Top X cyclical genes.</p>
<pre class="r"><code>topgenes_double <- readRDS(file="../data/results/ind_results_topgenes.rds")
topgenes_triple <- readRDS(file="../data/results/ind_results_topgenes_triple.rds")
topgenes_overlap <- sapply(1:length(topgenes_double), function(i) {
intersect(topgenes_double[[i]], topgenes_triple[[i]])
})
names(topgenes_overlap) <- names(topgenes_double)
plot(names(topgenes_double)[1:21],
sapply(topgenes_double, length)[1:21],
xlab="Top X cyclical genes", pch=16, col=1, cex=.7,
ylim=c(0,60),
ylab="Selected genes",
main = "Number of selected genes")
points(names(topgenes_double)[1:21],
sapply(topgenes_triple, length)[1:21], col="blue", pch=16, cex=.7)
points(names(topgenes_double)[1:21],
sapply(topgenes_overlap, length)[1:21], col="1", pch=1, cex=.7)
legend("topleft", legend=c("double", "triple", "both"),
col=c("black", "blue", "black"), pch=c(16, 16, 1))</code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-3-1.png" width="672" style="display: block; margin: auto;" /></p>
<hr />
</div>
<div id="prediction-error" class="section level2">
<h2>Prediction error</h2>
<p>summarize results</p>
<pre class="r"><code>diff_time_wrapper <- function(results_list) {
methods_list <- sapply(names(results_list),
function(x) strsplit(x, split=".", fixed=TRUE)[[1]][2])
diff_time_list <- do.call(rbind, lapply(1:length(results_list), function(i) {
diff_time <- results_list[[i]]$diff_time
diff_mean <- mean(diff_time/2/pi)
# diff_se <- sd(diff_time/2/pi)/sqrt(ncol(results_list[[1]]$Y))
return(data.frame(diff_mean=diff_mean,
# diff_se=diff_se,
methods=methods_list[i]))
}) )
return(diff_time_list)
}
library(gplots)
ngenes <- c(5, seq(10,200, by=10))
inds <- c("NA19098", "NA18511", "NA18870", "NA19101", "NA18855", "NA19160")
train_top <- lapply(1:length(inds), function(j) {
ind <- inds[j]
out <- do.call(rbind, lapply(1:length(ngenes), function(i) {
ngene <- ngenes[i]
train_topX <- do.call(rbind, lapply(1:5, function(fold) {
# print(ind)
# print(ngene)
# print(fold)
fl_name <- paste0("../data/results/ind_",ind,"_results_train.fold.",fold,
".top",ngene,".rds")
df <- readRDS(fl_name)
out <- diff_time_wrapper(df$fit.test)
out$fold <- fold
return(out)
}) )
train_topX$ngenes <- ngene
#return(train_topX)
agg_mn <- aggregate(diff_mean ~ methods,
data=train_topX, FUN=mean)
agg_sd <- aggregate(diff_mean ~ methods,
data=train_topX, FUN=sd)
obj <- data.frame(methods=agg_mn$methods,
diff_mean=agg_mn$diff_mean,
diff_se=agg_sd$diff_mean/sqrt(5))
obj$ngenes <- ngene
return(obj)
}) )
out$ind <- ind
return(out)
})
names(train_top) <- inds
saveRDS(train_top, file = "../output/method-train-ind.Rmd/diff_time_all.rds")
ngenes <- c(5, seq(10,200, by=10))
inds <- c("NA19098", "NA18511", "NA18870", "NA19101", "NA18855", "NA19160")
train_triple <- lapply(1:length(inds), function(j) {
ind <- inds[j]
out <- do.call(rbind, lapply(1:length(ngenes), function(i) {
ngene <- ngenes[i]
train_topX <- do.call(rbind, lapply(1:5, function(fold) {
# print(ind)
# print(ngene)
# print(fold)
fl_name <- paste0("../data/results/triple_ind_",ind,"_results_train.fold.",fold,
".top",ngene,".rds")
df <- readRDS(fl_name)
out <- diff_time_wrapper(df$fit.test)
out$fold <- fold
return(out)
}) )
train_topX$ngenes <- ngene
#return(train_topX)
agg_mn <- aggregate(diff_mean ~ methods,
data=train_topX, FUN=mean)
agg_sd <- aggregate(diff_mean ~ methods,
data=train_topX, FUN=sd)
obj <- data.frame(methods=agg_mn$methods,
diff_mean=agg_mn$diff_mean,
diff_se=agg_sd$diff_mean/sqrt(5))
obj$ngenes <- ngene
return(obj)
}) )
out$ind <- ind
return(out)
})
names(train_triple) <- inds
saveRDS(train_triple, file = "../output/method-train-ind.Rmd/diff_time_all_triple.rds")
# ngenes <- c(5, seq(10,200, by=10))
# train_top_permute <- do.call(rbind, lapply(1:length(ngenes), function(i) {
# ngene <- ngenes[i]
# train_topX <- do.call(rbind, lapply(1:5, function(fold) {
# fl_name <- paste0("../data/results/results_train_permute_oncyclical.fold.",
# fold,".top",ngene,".rds")
# df <- readRDS(fl_name)
# out <- diff_time_wrapper(df$fit.test)
# out$fold <- fold
# return(out)
# }) )
# train_topX$ngenes <- ngene
# #return(train_topX)
# agg_mn <- aggregate(diff_mean ~ methods,
# data=train_topX, FUN=mean)
# agg_sd <- aggregate(diff_mean ~ methods,
# data=train_topX, FUN=sd)
#
# obj <- data.frame(methods=agg_mn$methods,
# diff_mean=agg_mn$diff_mean,
# diff_se=agg_sd$diff_mean/sqrt(5))
# obj$ngenes <- ngene
# return(obj)
# }) )
#
# saveRDS(train_top_permute,
# file = "../output/method-train-classifiers-all.Rmd/diff_time_fucci_on_rando.rds")</code></pre>
<p>Results</p>
<pre class="r"><code>train_double <- readRDS("../output/method-train-ind.Rmd/diff_time_all.rds")
train_double <- do.call(rbind, train_double)
train_double <- subset(train_double, methods=="supervised")
train_double$ind <- as.factor(train_double$ind)
train_triple <- readRDS("../output/method-train-ind.Rmd/diff_time_all_triple.rds")
train_triple <- do.call(rbind, train_triple)
train_triple <- subset(train_triple, methods=="supervised")
train_triple$ind <- as.factor(train_triple$ind)</code></pre>
<p>time based on fucci</p>
<pre class="r"><code>library(ggplot2)
ggplot(train_double,
aes(x=ngenes, y=diff_mean, col=ind)) +
# geom_errorbar(train_top,
# mapping=aes(ymin=diff_mean-diff_se, ymax=diff_mean+diff_se,
# col=ind)) +
geom_point() + geom_line(lty=3) +
ylab("Error margin (% arc length)") + xlab("Top X cyclical genes") +
ggtitle("Prediction error in the training set") +
ylim(0,.25)</code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-5-1.png" width="672" style="display: block; margin: auto;" /></p>
<pre class="r"><code>ggplot(train_double,
aes(x=ngenes, y=diff_mean, col=ind)) +
# geom_errorbar(train_top,
# mapping=aes(ymin=diff_mean-diff_se, ymax=diff_mean+diff_se,
# col=ind)) +
geom_point() + geom_line(lty=3) +
ylab("Error margin (% arc length)") + xlab("Top X cyclical genes") +
ggtitle("Prediction error in the training set") </code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-5-2.png" width="672" style="display: block; margin: auto;" /></p>
<pre class="r"><code>ggplot(train_double,
aes(x=ngenes, y=diff_mean, col=ind)) +
geom_errorbar(train_double,
mapping=aes(ymin=diff_mean-diff_se, ymax=diff_mean+diff_se,
col=ind)) +
geom_point() + geom_line(lty=3) +
ylab("Error margin (% arc length)") + xlab("Top X cyclical genes") +
ggtitle("Prediction error in the training set") </code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-5-3.png" width="672" style="display: block; margin: auto;" /></p>
<p>time based on fucci + dapi</p>
<pre class="r"><code>library(ggplot2)
ggplot(train_triple,
aes(x=ngenes, y=diff_mean, col=ind)) +
# geom_errorbar(train_top,
# mapping=aes(ymin=diff_mean-diff_se, ymax=diff_mean+diff_se,
# col=ind)) +
geom_point() + geom_line(lty=3) +
ylab("Error margin (% arc length)") + xlab("Top X cyclical genes") +
ggtitle("Prediction error in the training set") +
ylim(0,.25)</code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-6-1.png" width="672" style="display: block; margin: auto;" /></p>
<pre class="r"><code>library(ggplot2)
ggplot(train_triple,
aes(x=ngenes, y=diff_mean, col=ind)) +
# geom_errorbar(train_top,
# mapping=aes(ymin=diff_mean-diff_se, ymax=diff_mean+diff_se,
# col=ind)) +
geom_point() + geom_line(lty=3) +
ylab("Error margin (% arc length)") + xlab("Top X cyclical genes") +
ggtitle("Prediction error in the training set") </code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-6-2.png" width="672" style="display: block; margin: auto;" /></p>
<pre class="r"><code>ggplot(train_triple,
aes(x=ngenes, y=diff_mean, col=ind)) +
geom_errorbar(train_double,
mapping=aes(ymin=diff_mean-diff_se, ymax=diff_mean+diff_se,
col=ind)) +
geom_point() + geom_line(lty=3) +
ylab("Error margin (% arc length)") + xlab("Top X cyclical genes") +
ggtitle("Prediction error in the training set") </code></pre>
<p><img src="figure/method-train-ind.Rmd/unnamed-chunk-6-3.png" width="672" style="display: block; margin: auto;" /></p>
<hr />
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_2.2.1 gplots_3.0.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 knitr_1.20 magrittr_1.5
[4] munsell_0.4.3 colorspace_1.3-2 rlang_0.1.6
[7] stringr_1.2.0 plyr_1.8.4 caTools_1.17.1
[10] tools_3.4.3 grid_3.4.3 gtable_0.2.0
[13] KernSmooth_2.23-15 git2r_0.21.0 htmltools_0.3.6
[16] gtools_3.5.0 lazyeval_0.2.1 yaml_2.1.16
[19] rprojroot_1.3-2 digest_0.6.15 tibble_1.4.2
[22] bitops_1.0-6 evaluate_0.10.1 rmarkdown_1.10
[25] labeling_0.3 gdata_2.18.0 stringi_1.1.6
[28] pillar_1.1.0 compiler_3.4.3 scales_0.5.0
[31] backports_1.1.2 </code></pre>
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