Illustrative example on running STM on TPM3 gene
DongyueXie
2023-03-12
Last updated: 2023-03-18
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Knit directory: SMF/
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Introduction
In this example, we illustrate running stm on TPM3 gene, per base pair reads from GTEX.
Model fitting
datax = read.csv('/project2/mstephens/gtex-stm/Counts/TPM3.Counts.csv.gz')
rownames(datax) = datax[,1]
datax = datax[,-1]
datax = as.matrix(datax)
datax = datax[,colSums(datax)!=0]
library(Matrix)
library(fastTopics)
X = Matrix(datax,sparse=T)
fit_fasttopics = fit_topic_model(X,k=7)
library(ebpmf)
tpm3_fit_fasttopics <- readRDS("~/Rpackages/gsmash/output/tpm3_fit_fasttopics.rds")
fit_stm = ebpmf_identity(datax,K=7,init = list(L_init = tpm3_fit_fasttopics$L,F_init = tpm3_fit_fasttopics$F))Visualize factors
fit_fasttopics = readRDS("~/Rpackages/gsmash/output/tpm3_fit_fasttopics.rds")
fit_stm = readRDS("~/Rpackages/gsmash/output/tpm3_fit_stm.rds")par(mfrow=c(2,1))
for(i in 1:7){
plot(fit_fasttopics$F[,i],col='grey50',pch='.',cex=2,type='l',xlab='position',ylab='',main=paste('topic model, factor', i))
plot(fit_stm$res$qf$Ef_smooth[,i],col='grey50',pch='.',cex=2,type='l',xlab='position',ylab='',main=paste('smoothed topic model, factor', i))
}
Visualize loadings Using structure plot
Post-processing factors
We see that there are spikes at the beginning/ending of exons. Large reads at the beginning/ending of exons may due to splitting reads.
To get a better visualization of smoothed factors, we can
post-process them using robust runmed method.
The function runmed(x,k) returns the running median of
x over window size k. We can tune \(k\) for each topic to achieve best
visualization. Here I choose \(k=43\).
Usually \(k\) between 11 to 111 should
be good.
par(mfrow=c(1,1))
for(k in 1:7){
plot(fit_stm$EF[,k],col='grey80',pch='.',cex=3,xlab='position',ylab='')
lines(runmed(fit_stm$EF[,k],k=43),type='l',col=1)
legend('topright',c('smoothed factors', 'post-processed using runmed'),pch=c(20,NA),lty=c(NA,1),col=c('grey80',1))
}
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /software/R-4.1.0-no-openblas-el7-x86_64/lib64/R/lib/libRblas.so
LAPACK: /software/R-4.1.0-no-openblas-el7-x86_64/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 rstudioapi_0.13 whisker_0.4 knitr_1.33
[5] magrittr_2.0.3 R6_2.5.1 rlang_1.0.6 fastmap_1.1.0
[9] fansi_1.0.4 highr_0.9 stringr_1.5.0 tools_4.1.0
[13] xfun_0.24 utf8_1.2.3 cli_3.6.0 git2r_0.28.0
[17] jquerylib_0.1.4 htmltools_0.5.4 rprojroot_2.0.2 yaml_2.3.7
[21] digest_0.6.31 tibble_3.1.8 lifecycle_1.0.3 later_1.3.0
[25] sass_0.4.0 vctrs_0.5.2 promises_1.2.0.1 fs_1.5.0
[29] glue_1.6.2 evaluate_0.14 rmarkdown_2.9 stringi_1.6.2
[33] bslib_0.2.5.1 compiler_4.1.0 pillar_1.8.1 jsonlite_1.8.4
[37] httpuv_1.6.1 pkgconfig_2.0.3