library(bigMap)

Load data

# first 50 principal components
load('./mcsk15.RData')

ptSNE

# +++ ./mcsk15/start.R

library(bigMap)
# +++ load data
load('~/omics/macosko15/mcsk.RData')
X <- mcsk15$clust_id
# +++ perplexities
ppx.list <- round(nrow(X) * c(.005, .01, .05, .10, .20, .30, .40, .50), 0)
# +++ run
m.list <- lapply(ppx.list, function(ppx)
{
    m <- bdm.init(X, ppx = ppx, threads = 20)
    m <- bdm.ptsne(X, m, theta = 0.5, threads = 20, layers = 2)
    m <- bdm.knp(X, m, threads = 20)
    m <- bdm.hlCorr(X, m, threads = 20)
    m
})
# +++ save
save(m.list, file = '~/omics/macosko15/bm456/mlist.RData')

Submit job:

$ qsub -pe make 20 -l h_vmem=4G Rsckt ./mcsk15/start.R

Load results

load('./mlist.RData')

Embedding cost/size function

nulL <- lapply(m.list, function(m) bdm.cost(m))

Embedding

nulL <- lapply(m.list, function(m) {
  m$lbls <- mcsk15$cell_type
  bdm.ptsne.plot(m, class.pltt = mcsk15$cell_type_pltt, ptsne.cex = 0.3)
})

hl-Correlation

hlTable <- sapply(m.list, function(m) summary(m$hlC)[4])
hlTable <- matrix(hlTable, nrow = 1)
colnames(hlTable) <- sapply(m.list, function(m) m$ppx$ppx)
rownames(hlTable) <- c('<hlC>')
knitr::kable(hlTable, caption = 'hl-Correlation') %>%
  kable_styling(full_width = F)
hl-Correlation
224 448 2240 4481 8962 13442 17923 22404
<hlC> 0.1325026 0.1582668 0.123278 0.1445667 0.1204305 0.2877653 0.2562428 0.2939314

Kary-neighborhood preservation

bdm.knp.plot(m.list)

Running Times

rTimes <- sapply(m.list, function(m) c(m$ppx$t[3], m$t$epoch, m$t$ptsne[3], (m$ppx$t[3] +m$t$ptsne[3])))
rTimes <- round(rTimes /60, 2)
colnames(rTimes) <- sapply(m.list, function(m) m$ppx$ppx)
rownames(rTimes) <- c('betas', 'epoch', 'ptsne', 'total')
knitr::kable(rTimes, caption = 'Computation times (min)') %>%
  kable_styling(full_width = F)
Computation times (min)
224 448 2240 4481 8962 13442 17923 22404
betas 0.13 0.13 0.19 0.24 0.36 0.47 0.51 0.51
epoch 0.06 0.06 0.08 0.10 0.15 0.20 0.21 0.21
ptsne 2.37 2.50 3.32 4.41 6.41 8.35 8.99 8.96
total 2.50 2.63 3.50 4.65 6.77 8.82 9.51 9.47

Intel(R) Xeon(R) CPU E5-2650 v3 2.30GHz, 32Mb cache, 20 cores, 4GB/core RAM.