Last updated: 2023-01-23
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Knit directory: gsmash/
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fit = readRDS('/project2/mstephens/dongyue/poisson_mf/droplet/ebpmf_droplet_vga3.rds')
load('/project2/mstephens/pcarbo/git/single-cell-topics/data/droplet.RData')
source('code/poisson_STM/plot_factors.R')
source('code/poisson_STM/plot_factors_general.R')
dim(counts)
[1] 7193 18388
table(samples$tissue)
Basal Ciliated Club Goblet Ionocyte
3845 425 2578 65 26
Neuroendocrine Tuft
96 158
fit$run_time
Time difference of 21.34445 hours
plot(fit$elbo_trace,type='l')
Version | Author | Date |
---|---|---|
eb3aa65 | DongyueXie | 2022-12-07 |
plot(fit$K_trace,type='l')
Version | Author | Date |
---|---|---|
eb3aa65 | DongyueXie | 2022-12-07 |
plot(fit$fit_flash$pve)
plot(fit$sigma2_trace[,which.max(fit$sigma2)],type='l',ylab='',main='convergence of largest sigma2')
round(unlist(lapply(fit$run_time_break_down,median)),3)
run_time_vga_init run_time_flash_init
176.656 186.724
run_time_vga run_time_flash_init_factor
44.425 22.808
run_time_flash_greedy run_time_flash_backfitting
0.000 78.932
run_time_flash_nullcheck
8.489
plot.factors(fit$fit_flash,samples$tissue,title='splitting PMF')
glmpca_nb = readRDS('/project2/mstephens/dongyue/poisson_mf/droplet/glmpca_droplet_nb.rds')
glmpca_poi = readRDS('/project2/mstephens/dongyue/poisson_mf/droplet/glmpca_droplet_poi.rds')
flash_fit = readRDS('/project2/mstephens/dongyue/poisson_mf/droplet/flash_droplet.rds')
plot.factors(flash_fit,samples$tissue,title='flash')
Version | Author | Date |
---|---|---|
eb3aa65 | DongyueXie | 2022-12-07 |
plot.factors.general(glmpca_poi$loadings,samples$tissue,title='glmpca pois')
Version | Author | Date |
---|---|---|
eb3aa65 | DongyueXie | 2022-12-07 |
plot.factors.general(glmpca_nb$loadings,samples$tissue,title='glmpca nb')
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] ggplot2_3.4.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 horseshoe_0.2.0 invgamma_1.1 lattice_0.20-44
[5] assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.30 utf8_1.2.2
[9] truncnorm_1.0-8 plyr_1.8.6 R6_2.5.1 evaluate_0.14
[13] highr_0.9 pillar_1.8.1 rlang_1.0.6 rstudioapi_0.13
[17] ebnm_1.0-11 irlba_2.3.5.1 whisker_0.4 jquerylib_0.1.4
[21] Matrix_1.5-3 rmarkdown_2.9 labeling_0.4.2 splines_4.1.0
[25] stringr_1.4.0 munsell_0.5.0 mixsqp_0.3-48 compiler_4.1.0
[29] httpuv_1.6.1 xfun_0.24 pkgconfig_2.0.3 SQUAREM_2021.1
[33] htmltools_0.5.3 tidyselect_1.2.0 tibble_3.1.8 fansi_1.0.3
[37] dplyr_1.0.10 withr_2.5.0 later_1.3.0 MASS_7.3-54
[41] grid_4.1.0 jsonlite_1.8.3 gtable_0.3.1 lifecycle_1.0.3
[45] DBI_1.1.1 git2r_0.28.0 magrittr_2.0.3 scales_1.2.1
[49] cli_3.5.0 stringi_1.6.2 farver_2.1.1 reshape2_1.4.4
[53] fs_1.5.0 promises_1.2.0.1 flashier_0.2.34 bslib_0.2.5.1
[57] generics_0.1.3 vctrs_0.5.1 trust_0.1-8 tools_4.1.0
[61] glmpca_0.2.0 glue_1.6.2 softImpute_1.4-1 parallel_4.1.0
[65] fastmap_1.1.0 yaml_2.3.6 colorspace_2.0-3 ashr_2.2-54
[69] deconvolveR_1.2-1 knitr_1.33 sass_0.4.0