Last updated: 2020-03-19

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Rmd 0cb8e9d Jason Willwerscheid 2020-03-19 wflow_publish(“analysis/pseudocount_redux_pbmc.Rmd”)

Introduction

I redo my previous analysis of pseudocounts using the PBMC 3k dataset. Fits were produced by adding 20 “greedy” factors and backfitting. The code can be viewed here.

source("./code/utils.R")
pbmc <- readRDS("./data/10x/pbmc.rds")
pbmc <- preprocess.pbmc(pbmc)
res <- readRDS("./output/pseudocount/pseudocount_fits_pbmc.rds")

Results: ELBO

As expected, the ELBO is monotonically decreasing as a function of the pseudocount.

elbo.df <- data.frame(pseudocount = as.numeric(names(res)),
                      elbo = sapply(res, function(x) x$fl$elbo + x$elbo.adj))
ggplot(elbo.df, aes(x = pseudocount, y = elbo)) +
  geom_point() +
  scale_x_continuous(trans = "log2") +
  labs(y = "ELBO")

Results: Log likelihood of implied distribution

An in the previous analysis, \(\alpha = 0.5\) does best.

llik.df <- data.frame(pseudocount = as.numeric(names(res)),
                      llik = sapply(res, function(x) x$p.vals$llik))
ggplot(llik.df, aes(x = pseudocount, y = llik)) +
  geom_point() +
  scale_x_continuous(trans = "log2") +
  labs(y = "log likelihood (implied model)")

Results: p-values

for (pc in names(res)) {
  cat("\n### Pseudocount = ", pc, "\n")
  plot(plot.p.vals(res[[pc]][["p.vals"]]))
  cat("\n")
}

Pseudocount = 0.0625

Pseudocount = 0.25

Pseudocount = 0.5

Pseudocount = 1

Pseudocount = 2

Pseudocount = 4

Pseudocount = 16



sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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     

other attached packages:
[1] flashier_0.2.4 ggplot2_3.2.0  Matrix_1.2-15 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        compiler_3.5.3    pillar_1.3.1     
 [4] git2r_0.25.2      workflowr_1.2.0   iterators_1.0.10 
 [7] tools_3.5.3       digest_0.6.18     evaluate_0.13    
[10] tibble_2.1.1      gtable_0.3.0      lattice_0.20-38  
[13] pkgconfig_2.0.2   rlang_0.4.2       foreach_1.4.4    
[16] parallel_3.5.3    yaml_2.2.0        ebnm_0.1-24      
[19] xfun_0.6          withr_2.1.2       stringr_1.4.0    
[22] dplyr_0.8.0.1     knitr_1.22        fs_1.2.7         
[25] rprojroot_1.3-2   grid_3.5.3        tidyselect_0.2.5 
[28] glue_1.3.1        R6_2.4.0          rmarkdown_1.12   
[31] mixsqp_0.3-31     irlba_2.3.3       ashr_2.2-38      
[34] purrr_0.3.2       magrittr_1.5      whisker_0.3-2    
[37] MASS_7.3-51.1     codetools_0.2-16  backports_1.1.3  
[40] scales_1.0.0      htmltools_0.3.6   assertthat_0.2.1 
[43] colorspace_1.4-1  labeling_0.3      stringi_1.4.3    
[46] pscl_1.5.2        doParallel_1.0.14 lazyeval_0.2.2   
[49] munsell_0.5.0     truncnorm_1.0-8   SQUAREM_2017.10-1
[52] crayon_1.3.4