DE analysis using a topic model: evaluation using simulated data
Peter Carbonetto
Last updated: 2021-10-13
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Knit directory: single-cell-topics/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6d63993 | Peter Carbonetto | 2021-10-13 | Made another simplification to simulate_twotopic_umi_data and added plots to de_analysis_detailed_look analysis comparing results with and without shrinkage. |
| Rmd | 157f7d3 | Peter Carbonetto | 2021-10-12 | Working on improved script driving_genes_better.R. |
| html | af856a2 | Peter Carbonetto | 2021-10-12 | Fixed the plots showing properties of the simulated data in the |
| Rmd | 2726a86 | Peter Carbonetto | 2021-10-12 | workflowr::wflow_publish(“de_analysis_detailed_look.Rmd”) |
| html | b8eadee | Peter Carbonetto | 2021-10-11 | Added some basic histograms to the de_analysis_detailed_look analysis. |
| Rmd | e2577f1 | Peter Carbonetto | 2021-10-11 | Working on the data simulation step in the de_analysis_detailed_look |
| html | cd17ccf | Peter Carbonetto | 2021-10-09 | Initial build of the de_analysis_detailed_look workflowr page. |
| Rmd | b8e1fe8 | Peter Carbonetto | 2021-10-09 | workflowr::wflow_publish(“de_analysis_detailed_look.Rmd”) |
| Rmd | 888ea7d | Peter Carbonetto | 2021-10-08 | I have an initial implementation of function simulate_twotopic_scrnaseq_data used to evaluate the de_analysis methods in fastTopics. |
Add summary of the analysis here.
Load the packages used in the analysis below, and some additional functions for simulating the data.
library(Matrix)
library(fastTopics)
library(ggplot2)
library(cowplot)
source("../code/de_eval_functions.R")Simulate UMI counts
We begin by simulating counts from a rank-2 Poisson NMF model with parameters chosen to roughly replicate the UMI counts obtained from a single-cell RNA sequencing experiment. In particular, we simulate counts \(x_{ij} \sim \mathrm{Poisson}(\lambda_{ij})\), such that \(\lambda_{ij} = \sum_{k=1}^K s_i l_{ik} f_{jk}\), with \(K = 2\), For now, we focus our attention on the \(K = 2\) case to simplify the analysis; comparing gene expression between three or topics brings some additional complications which aren’t necessary for assessing basic properties of the new DE methods. For more details on how the data are simulated, see function simulate_twotopic_umi_data.
set.seed(1)
dat <- simulate_twotopic_umi_data()
X <- dat$X
F <- dat$F
L <- dat$LBefore fitting a topic model and running a DE analysis, we first inspect some basic properties of the simulated data.
The sample sizes (total counts for each cell) in the simulated data are roughly normally distributed on the (base-10) log scale:
s <- rowSums(X)
p1 <- ggplot(data.frame(s = log10(s)),aes(x = s)) +
geom_histogram(color = "white",fill = "black",bins = 32) +
labs(x = "log10 size",y = "cells") +
theme_cowplot()
print(p1)
The expression rates were simulated so that they are normally distributed on the log scale:
p2 <- ggplot(data.frame(f = as.vector(F)),aes(x = log10(f))) +
geom_histogram(color = "white",fill = "black",bins = 32) +
labs(x = "log10 expression rate",y = "genes") +
theme_cowplot()
print(p2)
About half of the genes have nonzero differences in expression between the two topics. Among the nonzero gene expression differences, the log-fold changes (LFCs) were simulated from the normal distribution:
nonzero_lfc <- abs(F[,1] - F[,2]) > 1e-8
lfc <- log2(F[,1]/F[,2])
p3 <- ggplot(data.frame(lfc = lfc[nonzero_lfc]),aes(x = lfc)) +
geom_histogram(color = "white",fill = "black",bins = 32) +
labs(x = "LFC",y = "genes") +
theme_cowplot()
print(p3)
mean(nonzero_lfc)
# [1] 0.496
Fit multinomial topic model to UMI counts
Here we fit a multinomial topic model to the simulated UMI count data. To simplify evaluation of the DE methods, we assume that the topic proportions are known, and set to the ground truth (that is, the values used to simulate the data), so that the only error that can arise is in the estimates of the expression rates.
fit0 <- init_poisson_nmf(X,F = dat$F,L = with(dat,s*L))
fit <- fit_poisson_nmf(X,fit0 = fit0,numiter = 40,method = "scd",
update.loadings = NULL,verbose = "none")
# Using 4 RcppParallel threads.
fit <- poisson2multinom(fit)
summary(fit)
# Set show.size.factors = TRUE, show.mixprops = TRUE and/or show.topic.reps = TRUE in print(...) for more information
# Model overview:
# Number of data rows, n: 200
# Number of data cols, m: 10000
# Rank/number of topics, k: 2
# Evaluation of model fit (40 updates performed):
# Poisson NMF log-likelihood: -7.169037374429e+05
# Multinomial topic model log-likelihood: -7.158926302076e+05
# Poisson NMF deviance: +8.564731575439e+05
# Max KKT residual: +4.123695e-06DE analysis with and without shrinkage
First we perform a DE analysis without shrinking the LFC estimates:
set.seed(1)
de.noshrink <- de_analysis(fit,X,shrink.method = "none",
control = list(nc = 4))
# Using 4 RcppParallel threads.
# Using 4 SOCK threads.
# Progress bar cannot be shown when multithreading is used. For large data sets, the total runtime may be estimated by performing an initial test run with a small number of Monte Carlo samples, e.g., ns = 10; the total runtime should scale roughly linearly in ns, the number of Monte Carlo samples.
# Fitting 10000 Poisson models with k=2 using method="scd".
# Computing log-fold change statistics from 10000 Poisson models with k=2.Next we perform a second DE analysis using adaptive shrinkage to shrink (and hopefully improve accuracy of) the LFC estimates:
set.seed(1)
de <- de_analysis(fit,X,shrink.method = "ash",control = list(nc = 4))
# Using 4 RcppParallel threads.
# Using 4 SOCK threads.
# Progress bar cannot be shown when multithreading is used. For large data sets, the total runtime may be estimated by performing an initial test run with a small number of Monte Carlo samples, e.g., ns = 10; the total runtime should scale roughly linearly in ns, the number of Monte Carlo samples.
# Fitting 10000 Poisson models with k=2 using method="scd".
# Computing log-fold change statistics from 10000 Poisson models with k=2.
# Stabilizing posterior log-fold change estimates using adaptive shrinkage.Add text here.
pdat <- data.frame(noshrink = de.noshrink$postmean[,1],
shrink = de$postmean[,1],
log10mean = log10(de$f0))
p4 <- ggplot(pdat,aes(x = noshrink,y = shrink,fill = log10mean)) +
geom_point(shape = 21,color = "white") +
geom_abline(intercept = 0,slope = 1,color = "black",linetype = "dotted") +
scale_fill_gradient2(low = "deepskyblue",mid = "gold",high = "orangered",
midpoint = -3.5) +
xlim(c(-7,7.3)) +
ylim(c(-7,7.3)) +
labs(x = "original LFC estimates",
y = "shrunken LFC estimates") +
theme_cowplot()
print(p4)
Add text here.
pdat <- data.frame(noshrink = clamp(de.noshrink$z[,1],-4,+4),
shrink = clamp(de$z[,1],-4,+4),
de = factor(nonzero_lfc))
p5 <- ggplot(pdat,aes(x = noshrink,color = de,fill = de)) +
geom_histogram(bins = 64) +
scale_color_manual(values = c("darkorange","darkblue")) +
scale_fill_manual(values = c("darkorange","darkblue")) +
labs(x = "LFC estimate",y = "genes",title = "without shrinkage") +
theme_cowplot()
p6 <- ggplot(pdat,aes(x = shrink,color = de,fill = de)) +
geom_histogram(bins = 64) +
scale_color_manual(values = c("darkorange","darkblue")) +
scale_fill_manual(values = c("darkorange","darkblue")) +
labs(x = "LFC estimate",y = "genes",title = "with shrinkage") +
theme_cowplot()
print(plot_grid(p5,p6))
# Warning: Removed 6 rows containing non-finite values (stat_bin).
# Warning: Removed 6 rows containing non-finite values (stat_bin).
Add text here.
pdat <- data.frame(noshrink = 10^(-de.noshrink$lpval[,1]),
shrink = 10^(-de$lpval[,1]),
de = factor(nonzero_lfc))
p7 <- ggplot(pdat,aes(x = noshrink,color = de,fill = de)) +
geom_histogram(bins = 64) +
scale_color_manual(values = c("darkorange","darkblue")) +
scale_fill_manual(values = c("darkorange","darkblue")) +
labs(x = "p-value",y = "genes",title = "without shrinkage") +
theme_cowplot()
p8 <- ggplot(pdat,aes(x = shrink,color = de,fill = de)) +
geom_histogram(bins = 64) +
scale_color_manual(values = c("darkorange","darkblue")) +
scale_fill_manual(values = c("darkorange","darkblue")) +
labs(x = "p-value",y = "genes",title = "with shrinkage") +
theme_cowplot()
print(plot_grid(p7,p8))
# Warning: Removed 6 rows containing non-finite values (stat_bin).
# Warning: Removed 6 rows containing non-finite values (stat_bin).
sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
#
# Matrix products: default
# BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] cowplot_1.0.0 ggplot2_3.3.5 fastTopics_0.6-70 Matrix_1.2-18
#
# loaded via a namespace (and not attached):
# [1] httr_1.4.2 tidyr_1.1.3 jsonlite_1.7.2 viridisLite_0.3.0
# [5] RcppParallel_4.4.2 assertthat_0.2.1 mixsqp_0.3-46 yaml_2.2.0
# [9] progress_1.2.2 ggrepel_0.9.1 pillar_1.6.2 backports_1.1.5
# [13] lattice_0.20-38 quantreg_5.54 glue_1.4.2 quadprog_1.5-8
# [17] digest_0.6.23 promises_1.1.0 colorspace_1.4-1 htmltools_0.4.0
# [21] httpuv_1.5.2 pkgconfig_2.0.3 invgamma_1.1 SparseM_1.78
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# [37] ashr_2.2-51 lazyeval_0.2.2 magrittr_2.0.1 crayon_1.4.1
# [41] mcmc_0.9-6 evaluate_0.14 fs_1.3.1 fansi_0.4.0
# [45] MASS_7.3-51.4 truncnorm_1.0-8 tools_3.6.2 data.table_1.12.8
# [49] prettyunits_1.1.1 hms_1.1.0 lifecycle_1.0.0 stringr_1.4.0
# [53] MCMCpack_1.4-5 plotly_4.9.2 munsell_0.5.0 irlba_2.3.3
# [57] compiler_3.6.2 rlang_0.4.11 grid_3.6.2 htmlwidgets_1.5.1
# [61] labeling_0.3 rmarkdown_2.3 gtable_0.3.0 DBI_1.1.0
# [65] R6_2.4.1 knitr_1.26 dplyr_1.0.7 utf8_1.1.4
# [69] workflowr_1.6.2 rprojroot_1.3-2 stringi_1.4.3 parallel_3.6.2
# [73] SQUAREM_2017.10-1 Rcpp_1.0.7 vctrs_0.3.8 tidyselect_1.1.1
# [77] xfun_0.11 coda_0.19-3