Last updated: 2021-10-04
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Knit directory: SMF/
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| File | Version | Author | Date | Message |
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| Rmd | 1a63658 | DongyueXie | 2021-10-04 | wflow_publish(“analysis/integration_stm.Rmd”) |
| html | 30b4333 | DongyueXie | 2021-10-04 | Build site. |
| Rmd | 2566f86 | DongyueXie | 2021-10-04 | wflow_publish(“analysis/integration_stm.Rmd”) |
#'@param EF a p by K factor matrix
#'@param k #factors to be plot
plot_factor = function(EF,k,main=NULL){
plot(EF[,1],type='l',ylab='',xlab='base',main=main,ylim=range(EF))
if(k>1){
for(i in 2:k){
lines(EF[,i],col=i,lty=i)
}
}
}
# summary_study = function(fit,K,method='stm'){
# # plot factors
# p = ncol(fit$X)
# idx1 = 1:(p/3)
# idx2 = (p/3+1):(p/3*2)
# idx3 = (p/3*2+1):(p)
# if(method=='stm'){
# EF = fit$fit_stm$EF
# }else if(method=='NMF'){
# EF = t(fit$fit_NMF$H)
# }else if(method=='hals'){
# EF = t(fit$fit_hals$V)
# }
# for(k in 1:K){
# plot(EF[idx1,k],type='l',ylab='',xlab='base',main=paste('factor ',k),ylim=range(EF[,k]),col=2)
# lines(EF[idx2,k],col=3,xlab='base')
# lines(EF[idx3,k],col=4,xlab='base')
# legend('topright',c("RNA","H3K4me1","ATAC"),lty=c(1,1,1),col=c(2,3,4))
# }
# }
#'@param K number of factors to be plot
summary_study = function(fit,K,gene=NULL,method='stm'){
# plot factors
p = ncol(fit$X)
idx1 = 1:(p/3)
idx2 = (p/3+1):(p/3*2)
idx3 = (p/3*2+1):(p)
if(method=='stm'){
EF = fit$fit_stm$EF
}else if(method=='NMF'){
EF = t(fit$fit_NMF$H)
}else if(method=='hals'){
EF = t(fit$fit_hals$V)
}
par(mfrow=c(3,1))
for(k in 1:K){
plot(EF[idx1,k],type='l',ylab='',xlab='base',main=c(paste(gene, 'factor',k),'RNA'),col=2)
plot(EF[idx2,k],col=3,xlab='base',ylab='',type='l',main='H3K4me1')
plot(EF[idx3,k],col=4,xlab='base',ylab='',type='l',main='ATAC')
}
}files = list.files('/project2/mstephens/dongyue/luis/luis')
genes = c()
for(i in 1:length(files)){
genes[i] = strsplit(files[i],split = '_')[[1]][1]
}
genes = unique(genes)
genes = genes[-which(genes=='MRPL18')]for(gene in genes){
print(gene)
fit = readRDS(paste('output/luis/',gene,'_K10_merge10base.rds',sep=''))
summary_study(fit,K = 10,gene=gene)
}# for(gene in genes){
# print(gene)
# fit = readRDS(paste('output/luis/',gene,'_K10_merge10base.rds',sep=''))
# summary_study(fit,K = 10,gene=gene,method = 'NMF')
# }
gene = genes[1]
fit = readRDS(paste('output/luis/',gene,'_K10_merge10base.rds',sep=''))
method='stm'
K = 10
p = ncol(fit$X)Loading required package: Matrix # idx1 = 1:(p/3)
# idx2 = (p/3+1):(p/3*2)
# idx3 = (p/3*2+1):(p)
# if(method=='stm'){
# EF = fit$fit_stm$EF
# }else if(method=='NMF'){
# EF = t(fit$fit_NMF$H)
# }else if(method=='hals'){
# EF = t(fit$fit_hals$V)
# }
# par(mfrow=c(3,1))
# for(k in 1:K){
# plot(EF[idx1,k],type='l',ylab='',xlab='base',main=c(paste(gene, 'factor',k),'RNA'),col=2)
# plot(EF[idx2,k],col=3,xlab='base',ylab='',type='l',main='H3K4me1')
# plot(EF[idx3,k],col=4,xlab='base',ylab='',type='l',main='ATAC')
# }
sessionInfo()R version 3.6.1 (2019-07-05)
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] Matrix_1.2-18 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lattice_0.20-38 rprojroot_2.0.2 digest_0.6.20
[5] later_0.8.0 grid_3.6.1 R6_2.4.0 git2r_0.26.1
[9] magrittr_1.5 evaluate_0.14 stringi_1.4.3 fs_1.3.1
[13] promises_1.0.1 whisker_0.3-2 rmarkdown_1.13 tools_3.6.1
[17] stringr_1.4.0 glue_1.3.1 httpuv_1.5.1 xfun_0.8
[21] yaml_2.2.0 compiler_3.6.1 htmltools_0.3.6 knitr_1.23