Last updated: 2020-02-12

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Knit directory: SMF/

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~/SMF/data/RPS13_hals_runmed_K3.RData data/RPS13_hals_runmed_K3.RData
~/SMF/data/RPS13_hals_wavelet_K3.RData data/RPS13_hals_wavelet_K3.RData
~/SMF/data/RPS13_stm_nugget_robust_K3.RData data/RPS13_stm_nugget_robust_K3.RData
~/SMF/data/RPS13_stm_nugget_K3.RData data/RPS13_stm_nugget_K3.RData
~/SMF/data/RPS13_stm_bmsm_K3.RData data/RPS13_stm_bmsm_K3.RData
~/SMF/data/RPS13_NMF_mkl_scd_K3.RData data/RPS13_NMF_mkl_scd_K3.RData
~/SMF/data/GPX3_hals_runmed_K3.RData data/GPX3_hals_runmed_K3.RData
~/SMF/data/GPX3_hals_wavelet_K3.RData data/GPX3_hals_wavelet_K3.RData
~/SMF/data/GPX3_stm_nugget_robust_K3.RData data/GPX3_stm_nugget_robust_K3.RData
~/SMF/data/GPX3_stm_nugget_K3.RData data/GPX3_stm_nugget_K3.RData
~/SMF/data/GPX3_stm_bmsm_K3.RData data/GPX3_stm_bmsm_K3.RData
~/SMF/data/GPX3_NMF_mkl_scd_K3.RData data/GPX3_NMF_mkl_scd_K3.RData
~/SMF/data/PSAP_hals_runmed_K3.RData data/PSAP_hals_runmed_K3.RData
~/SMF/data/PSAP_hals_wavelet_K3.RData data/PSAP_hals_wavelet_K3.RData
~/SMF/data/PSAP_stm_nugget_robust_K3.RData data/PSAP_stm_nugget_robust_K3.RData
~/SMF/data/PSAP_stm_nugget_K3.RData data/PSAP_stm_nugget_K3.RData
~/SMF/data/PSAP_stm_bmsm_K3.RData data/PSAP_stm_bmsm_K3.RData
~/SMF/data/PSAP_NMF_mkl_scd_K3.RData data/PSAP_NMF_mkl_scd_K3.RData
~/SMF/data/RPS13_hals_runmed_K3_base5.RData data/RPS13_hals_runmed_K3_base5.RData
~/SMF/data/RPS13_hals_wavelet_K3_base5.RData data/RPS13_hals_wavelet_K3_base5.RData
~/SMF/data/RPS13_stm_nugget_robust_K3_base5.RData data/RPS13_stm_nugget_robust_K3_base5.RData
~/SMF/data/RPS13_stm_nugget_K3_base5.RData data/RPS13_stm_nugget_K3_base5.RData
~/SMF/data/RPS13_stm_bmsm_K3_base5.RData data/RPS13_stm_bmsm_K3_base5.RData
~/SMF/data/RPS13_NMF_mkl_scd_K3_base5.RData data/RPS13_NMF_mkl_scd_K3_base5.RData
~/SMF/data/GPX3_hals_runmed_K3_base5.RData data/GPX3_hals_runmed_K3_base5.RData
~/SMF/data/GPX3_hals_wavelet_K3_base5.RData data/GPX3_hals_wavelet_K3_base5.RData
~/SMF/data/GPX3_stm_nugget_robust_K3_base5.RData data/GPX3_stm_nugget_robust_K3_base5.RData
~/SMF/data/GPX3_stm_nugget_K3_base5.RData data/GPX3_stm_nugget_K3_base5.RData
~/SMF/data/GPX3_stm_bmsm_K3_base5.RData data/GPX3_stm_bmsm_K3_base5.RData
~/SMF/data/GPX3_NMF_mkl_scd_K3_base5.RData data/GPX3_NMF_mkl_scd_K3_base5.RData
~/SMF/data/PSAP_hals_runmed_K3_base5.RData data/PSAP_hals_runmed_K3_base5.RData
~/SMF/data/PSAP_hals_wavelet_K3_base5.RData data/PSAP_hals_wavelet_K3_base5.RData
~/SMF/data/PSAP_stm_nugget_robust_K3_base5.RData data/PSAP_stm_nugget_robust_K3_base5.RData
~/SMF/data/PSAP_stm_nugget_K3_base5.RData data/PSAP_stm_nugget_K3_base5.RData
~/SMF/data/PSAP_stm_bmsm_K3_base5.RData data/PSAP_stm_bmsm_K3_base5.RData
~/SMF/data/PSAP_NMF_mkl_scd_K3_base5.RData data/PSAP_NMF_mkl_scd_K3_base5.RData
~/SMF/data/RPS13_hals_runmed_K3_base10.RData data/RPS13_hals_runmed_K3_base10.RData
~/SMF/data/RPS13_hals_wavelet_K3_base10.RData data/RPS13_hals_wavelet_K3_base10.RData
~/SMF/data/RPS13_stm_nugget_robust_K3_base10.RData data/RPS13_stm_nugget_robust_K3_base10.RData
~/SMF/data/RPS13_stm_nugget_K3_base10.RData data/RPS13_stm_nugget_K3_base10.RData
~/SMF/data/RPS13_stm_bmsm_K3_base10.RData data/RPS13_stm_bmsm_K3_base10.RData
~/SMF/data/RPS13_NMF_mkl_scd_K3_base10.RData data/RPS13_NMF_mkl_scd_K3_base10.RData
~/SMF/data/GPX3_hals_runmed_K3_base10.RData data/GPX3_hals_runmed_K3_base10.RData
~/SMF/data/GPX3_hals_wavelet_K3_base10.RData data/GPX3_hals_wavelet_K3_base10.RData
~/SMF/data/GPX3_stm_nugget_robust_K3_base10.RData data/GPX3_stm_nugget_robust_K3_base10.RData
~/SMF/data/GPX3_stm_nugget_K3_base10.RData data/GPX3_stm_nugget_K3_base10.RData
~/SMF/data/GPX3_stm_bmsm_K3_base10.RData data/GPX3_stm_bmsm_K3_base10.RData
~/SMF/data/GPX3_NMF_mkl_scd_K3_base10.RData data/GPX3_NMF_mkl_scd_K3_base10.RData
~/SMF/data/PSAP_hals_runmed_K3_base10.RData data/PSAP_hals_runmed_K3_base10.RData
~/SMF/data/PSAP_hals_wavelet_K3_base10.RData data/PSAP_hals_wavelet_K3_base10.RData
~/SMF/data/PSAP_stm_nugget_robust_K3_base10.RData data/PSAP_stm_nugget_robust_K3_base10.RData
~/SMF/data/PSAP_stm_nugget_K3_base10.RData data/PSAP_stm_nugget_K3_base10.RData
~/SMF/data/PSAP_stm_bmsm_K3_base10.RData data/PSAP_stm_bmsm_K3_base10.RData
~/SMF/data/PSAP_NMF_mkl_scd_K3_base10.RData data/PSAP_NMF_mkl_scd_K3_base10.RData

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Untracked files:
    Untracked:  code/GTEx_Splicing.R
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Unstaged changes:
    Modified:   analysis/GTExSplicing.Rmd
    Modified:   analysis/index.Rmd
    Deleted:    code/BMSM.R
    Deleted:    code/EBMPMF.R
    Deleted:    code/ebbp_beta_mixture.R
    Modified:   code/ebpm_exp_mixture.R
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    Deleted:    code/update_l.R

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Rmd 1106b97 DongyueXie 2020-02-12 wflow_publish(“analysis/stmGTEx.Rmd”)
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per base read count

RPS13

library(stm)
load("~/SMF/data/RPS13_hals_runmed_K3.RData")
load("~/SMF/data/RPS13_hals_wavelet_K3.RData")
load("~/SMF/data/RPS13_stm_nugget_robust_K3.RData")
load("~/SMF/data/RPS13_stm_nugget_K3.RData")
load("~/SMF/data/RPS13_stm_bmsm_K3.RData")
load("~/SMF/data/RPS13_NMF_mkl_scd_K3.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.008),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

GPX3

load("~/SMF/data/GPX3_hals_runmed_K3.RData")
load("~/SMF/data/GPX3_hals_wavelet_K3.RData")
load("~/SMF/data/GPX3_stm_nugget_robust_K3.RData")
load("~/SMF/data/GPX3_stm_nugget_K3.RData")
load("~/SMF/data/GPX3_stm_bmsm_K3.RData")
load("~/SMF/data/GPX3_NMF_mkl_scd_K3.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.005),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01

PSAP

load("~/SMF/data/PSAP_hals_runmed_K3.RData")
load("~/SMF/data/PSAP_hals_wavelet_K3.RData")
load("~/SMF/data/PSAP_stm_nugget_robust_K3.RData")
load("~/SMF/data/PSAP_stm_nugget_K3.RData")
load("~/SMF/data/PSAP_stm_bmsm_K3.RData")
load("~/SMF/data/PSAP_NMF_mkl_scd_K3.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
2fee345 DongyueXie 2019-12-01
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.002),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
2fee345 DongyueXie 2019-12-01
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
2fee345 DongyueXie 2019-12-01
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

per 5 base count sum

RPS13

load("~/SMF/data/RPS13_hals_runmed_K3_base5.RData")
load("~/SMF/data/RPS13_hals_wavelet_K3_base5.RData")
load("~/SMF/data/RPS13_stm_nugget_robust_K3_base5.RData")
load("~/SMF/data/RPS13_stm_nugget_K3_base5.RData")
load("~/SMF/data/RPS13_stm_bmsm_K3_base5.RData")
load("~/SMF/data/RPS13_NMF_mkl_scd_K3_base5.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_wavelet$V),fit_hals_wavelet$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS wavelet')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

summary(lf$FF[,3])
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.001387 0.001460 0.001528 0.001524 0.001597 0.001626

GPX3

load("~/SMF/data/GPX3_hals_runmed_K3_base5.RData")
load("~/SMF/data/GPX3_hals_wavelet_K3_base5.RData")
load("~/SMF/data/GPX3_stm_nugget_robust_K3_base5.RData")
load("~/SMF/data/GPX3_stm_nugget_K3_base5.RData")
load("~/SMF/data/GPX3_stm_bmsm_K3_base5.RData")
load("~/SMF/data/GPX3_NMF_mkl_scd_K3_base5.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_wavelet$V),fit_hals_wavelet$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS wavelet')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01

PSAP

load("~/SMF/data/PSAP_hals_runmed_K3_base5.RData")
load("~/SMF/data/PSAP_hals_wavelet_K3_base5.RData")
load("~/SMF/data/PSAP_stm_nugget_robust_K3_base5.RData")
load("~/SMF/data/PSAP_stm_nugget_K3_base5.RData")
load("~/SMF/data/PSAP_stm_bmsm_K3_base5.RData")
load("~/SMF/data/PSAP_NMF_mkl_scd_K3_base5.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.03),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_wavelet$V),fit_hals_wavelet$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS wavelet')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

per 10 base count sum

RPS13

library(stm)
load("~/SMF/data/RPS13_hals_runmed_K3_base10.RData")
load("~/SMF/data/RPS13_hals_wavelet_K3_base10.RData")
load("~/SMF/data/RPS13_stm_nugget_robust_K3_base10.RData")
load("~/SMF/data/RPS13_stm_nugget_K3_base10.RData")
load("~/SMF/data/RPS13_stm_bmsm_K3_base10.RData")
load("~/SMF/data/RPS13_NMF_mkl_scd_K3_base10.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.4),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_wavelet$V),fit_hals_wavelet$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS wavelet')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01

GPX3

load("~/SMF/data/GPX3_hals_runmed_K3_base10.RData")
load("~/SMF/data/GPX3_hals_wavelet_K3_base10.RData")
load("~/SMF/data/GPX3_stm_nugget_robust_K3_base10.RData")
load("~/SMF/data/GPX3_stm_nugget_K3_base10.RData")
load("~/SMF/data/GPX3_stm_bmsm_K3_base10.RData")
load("~/SMF/data/GPX3_NMF_mkl_scd_K3_base10.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.15),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_hals_wavelet$V),fit_hals_wavelet$U)
plot(lf$FF[,1],col=2,ylim=c(0,0.05),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS wavelet')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

PSAP

load("~/SMF/data/PSAP_hals_runmed_K3_base10.RData")
load("~/SMF/data/PSAP_hals_wavelet_K3_base10.RData")
load("~/SMF/data/PSAP_stm_nugget_robust_K3_base10.RData")
load("~/SMF/data/PSAP_stm_nugget_K3_base10.RData")
load("~/SMF/data/PSAP_stm_bmsm_K3_base10.RData")
load("~/SMF/data/PSAP_NMF_mkl_scd_K3_base10.RData")

lf = poisson2multinom(t(fit_NMF$H),fit_NMF$W)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - NMF scd mKL')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm$qf),fit_stm$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smooth')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_runmed$V),fit_hals_runmed$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS runmed')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_hals_wavelet$V),fit_hals_wavelet$U)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - HALS wavelet')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget$qf),fit_stm_nugget$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 
lf = poisson2multinom(t(fit_stm_nugget_robust$qf),fit_stm_nugget_robust$ql)
plot(lf$FF[,1],col=2,ylim=range(lf$FF),type='l',xlab = 'base',ylab='Intensity',main='Factors - smashgen robust')
lines(lf$FF[,2],col=3)
lines(lf$FF[,3],col=4)

Version Author Date
83dd0db DongyueXie 2019-12-01 

sessionInfo()
R version 3.5.1 (2018-07-02)
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] stm_1.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        compiler_3.5.1    later_0.7.5      
 [4] git2r_0.26.1      highr_0.7         workflowr_1.6.0  
 [7] bitops_1.0-6      iterators_1.0.10  tools_3.5.1      
[10] digest_0.6.18     evaluate_0.12     lattice_0.20-38  
[13] pkgconfig_2.0.2   igraph_1.2.2      Matrix_1.2-15    
[16] foreach_1.4.4     yaml_2.2.0        parallel_3.5.1   
[19] smashr_1.2-7      stringr_1.3.1     knitr_1.20       
[22] caTools_1.17.1.1  fs_1.3.1          gtools_3.8.1     
[25] rprojroot_1.3-2   grid_3.5.1        data.table_1.12.0
[28] glue_1.3.0        R6_2.3.0          rmarkdown_1.10   
[31] genlasso_1.4      mixsqp_0.2-2      ashr_2.2-39      
[34] magrittr_1.5      whisker_0.3-2     backports_1.1.2  
[37] promises_1.0.1    codetools_0.2-15  htmltools_0.3.6  
[40] MASS_7.3-51.1     httpuv_1.4.5      wavethresh_4.6.8 
[43] stringi_1.2.4     doParallel_1.0.14 pscl_1.5.2       
[46] truncnorm_1.0-8   NNLM_0.4.2        SQUAREM_2017.10-1
[49] ebpm_0.0.0.9004