example_yusha_sc

Last updated: 2022-07-21

Checks: 7 0

Knit directory: logistic-susie-gsea/

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Ignored files:
    Ignored:    .DS_Store
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    Ignored:    .Rproj.user/
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    Ignored:    _targets.html
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    Ignored:    data/adipose_2yr_topsnp.txt
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    Ignored:    data/de-microplastics/
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    Ignored:    data/fetal_reference_cellid_gene_sets.RData
    Ignored:    data/human_chimp_eb/
    Ignored:    data/pbmc-purified/
    Ignored:    data/wenhe_baboon_diet/
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Untracked files:
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    Untracked:  Master's Paper.pdf
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    Untracked:  Project_1653228324/
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    Untracked:  _targets/meta/
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    Untracked:  analysis/alpha_ash_v_point_normal.Rmd
    Untracked:  analysis/compare_w_post_hoc_clustering.Rmd
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    Untracked:  analysis/de_droplet_noshrink_logistic_susie.Rmd
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    Untracked:  analysis/logistic_variational_bound.Rmd
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File	Version	Author	Date	Message
Rmd	4872e81	karltayeb	2022-07-21	wflow_publish("analysis/example_mellissa_microplastics.Rmd")
html	4b8c5d1	karltayeb	2022-07-21	Build site.
Rmd	3e90f1a	karltayeb	2022-07-21	wflow_publish("analysis/example_mellissa_microplastics.Rmd")

Load data

source('code/load_data.R')

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──

✔ ggplot2 3.3.6     ✔ purrr   0.3.4
✔ tibble  3.1.7     ✔ dplyr   1.0.9
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.2     ✔ forcats 0.5.1

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(gseasusie)

# save output to a folder... helps for running many factors
cache_rds = purrr::partial(xfun::cache_rds, dir='cache/de_microplastics/')



driver = function(gs, experiment){
  dat <- gseasusie::prep_binary_data(gs, data[[experiment]])
  ora <- gseasusie::fit_ora(dat$X, dat$y)
  # add description
  ora <- ora %>%
    dplyr::left_join(gs$geneSetDes)
  fit <- gseasusie::fit_logistic_susie_veb_boost(dat$X, dat$y)
  return(list(fit=fit, ora=ora))
}

driver_cached = function(prefix, gs, experiment){
  file = paste0(prefix, '_', gs$db, '_', experiment, '.rds')
  print(file)
  cache_rds(driver(gs, experiment), file=file)
}

data <- read_rds('data/de-microplastics/plastics_de.rds')
map2enrtrez <- generate_map2entrez(rownames(data$`0`$fivemg), 'SYMBOL')

'select()' returned 1:many mapping between keys and columns

data <- unlist(data, recursive = F)
data <- purrr::map(data, ~ rownames_to_column(.x, 'SYMBOL') %>% 
                     mutate(beta = 1, threshold.on = (p_val_adj * as.integer(row_number() > 2))) %>% 
                     left_join(map2enrtrez))

Joining, by = "SYMBOL"

Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
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Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
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Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
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Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
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Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"
Joining, by = "SYMBOL"

go <- gseasusie::load_all_go()

loading gene set from webgestaltr: geneontology_Biological_Process
loading gene set from webgestaltr: geneontology_Molecular_Function
loading gene set from webgestaltr: geneontology_Cellular_Component

res <- purrr::map(names(data), ~driver_cached('microplastics', go, .x))

[1] "microplastics_all_go_0.fivemg.rds"
[1] "microplastics_all_go_0.twentymg.rds"
[1] "microplastics_all_go_0.twentymg2x.rds"
[1] "microplastics_all_go_0.hundredmg.rds"
[1] "microplastics_all_go_1.fivemg.rds"
[1] "microplastics_all_go_1.twentymg.rds"
[1] "microplastics_all_go_1.twentymg2x.rds"
[1] "microplastics_all_go_1.hundredmg.rds"
[1] "microplastics_all_go_2.fivemg.rds"
[1] "microplastics_all_go_2.twentymg.rds"
[1] "microplastics_all_go_2.twentymg2x.rds"
[1] "microplastics_all_go_2.hundredmg.rds"
[1] "microplastics_all_go_3.fivemg.rds"
[1] "microplastics_all_go_3.twentymg.rds"
[1] "microplastics_all_go_3.twentymg2x.rds"
[1] "microplastics_all_go_3.hundredmg.rds"
[1] "microplastics_all_go_4.fivemg.rds"
[1] "microplastics_all_go_4.twentymg.rds"
[1] "microplastics_all_go_4.twentymg2x.rds"
[1] "microplastics_all_go_4.hundredmg.rds"
[1] "microplastics_all_go_5.fivemg.rds"
[1] "microplastics_all_go_5.twentymg.rds"
[1] "microplastics_all_go_5.twentymg2x.rds"
[1] "microplastics_all_go_5.hundredmg.rds"
[1] "microplastics_all_go_6.fivemg.rds"
[1] "microplastics_all_go_6.twentymg.rds"
[1] "microplastics_all_go_6.twentymg2x.rds"
[1] "microplastics_all_go_6.hundredmg.rds"

names(res) <- names(data)

results <- res
experiments <- names(results)

safe_static_table <- purrr::safely(
  gseasusie::static_table,
  otherwise = 'nothing to report')

for(this_experiment in experiments){
  sub_res <- results[[this_experiment]]
  volcano <- gseasusie::enrichment_volcano(fit=sub_res$fit, ora=sub_res$ora)
  results[[this_experiment]]$volcano <- volcano
  
  table <- safe_static_table(sub_res$fit, sub_res$ora)$result
  results[[this_experiment]]$table <- table
}

cat('\n')

cat('##', 'Results')

Results

for(this_experiment in experiments){
  cat('\n')
  cat('###', this_experiment)

  #sub_res <- results[[this_experiment]]
  #volcano <- gseasusie::enrichment_volcano(fit=sub_res$fit, ora=sub_res$ora)
  print(results[[this_experiment]]$volcano)
  
  cat("\n\n")
  #table <- safe_static_table(sub_res$fit, sub_res$ora)$result
  print(results[[this_experiment]]$table)
}

0.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	94	36	10.1	7.81	0.993	0.993	73.9	1

0.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

0.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	94	45	6.41	6.13	0.984	0.984	59.2	1

0.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	94	77	6.12	7.06	1	1	74.2	1
L2
GO:0044421	extracellular region part	2600	346	1.48	1.2	1	1	42.6	17
L4
GO:0048468	cell development	1840	222	1.14	1	1	1	19.6	61
L3
GO:0006616	SRP-dependent cotranslational protein targeting to membrane, translocation	11	1	0.5	-5.89	0.999	0.999	0.277	5340

1.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

1.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

1.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

1.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006613	cotranslational protein targeting to membrane	98	78	4.64	4.14	0.482	0.482	47.9	1
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	94	76	4.75	4.23	0.513	0.513	47.6	2
L2
GO:0044421	extracellular region part	2520	571	1.07	0.873	1	1	38	7
L6
GO:0070161	anchoring junction	530	168	1.59	0.914	0.516	0.516	25.7	16
GO:0005912	adherens junction	517	165	1.61	0.923	0.479	0.479	25.7	17
L4
GO:0044432	endoplasmic reticulum part	1160	279	1.06	0.949	0.998	0.998	20.9	31
L3
GO:0051301	cell division	540	156	1.39	1.04	1	1	19.4	39
L5
GO:0000779	condensed chromosome, centromeric region	112	49	2.29	1.89	0.716	0.716	13.8	60
GO:0000793	condensed chromosome	206	71	1.73	1.43	0.255	0.256	13	64
L8
GO:0008219	cell death	1820	359	0.697	0.49	0.43	0.43	12.4	71
GO:0012501	programmed cell death	1700	340	0.711	0.5	0.356	0.356	12.2	74
GO:0006915	apoptotic process	1650	328	0.702	0.501	0.212	0.213	11.7	79

2.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

2.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

2.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

2.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	94	25	6.62	6.16	0.966	0.966	36.1	1

3.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

3.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

3.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

3.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

4.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

4.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

4.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

4.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

5.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

5.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

5.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

5.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

6.fivemg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

6.twentymg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

6.twentymg2x

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

6.hundredmg

Version	Author	Date
4b8c5d1	karltayeb	2022-07-21

[1] “nothing to report”

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] gseasusie_0.0.0.9000 forcats_0.5.1        stringr_1.4.0       
 [4] dplyr_1.0.9          purrr_0.3.4          readr_2.1.2         
 [7] tidyr_1.2.0          tibble_3.1.7         ggplot2_3.3.6       
[10] tidyverse_1.3.1     

loaded via a namespace (and not attached):
  [1] matrixStats_0.62.0     bitops_1.0-7           fs_1.5.2              
  [4] lubridate_1.8.0        bit64_4.0.5            webshot_0.5.3         
  [7] httr_1.4.3             rprojroot_2.0.3        GenomeInfoDb_1.30.1   
 [10] data.tree_1.0.0        tools_4.1.2            backports_1.4.1       
 [13] bslib_0.3.1            utf8_1.2.2             R6_2.5.1              
 [16] DBI_1.1.2              BiocGenerics_0.40.0    colorspace_2.0-3      
 [19] withr_2.5.0            tidyselect_1.1.2       bit_4.0.4             
 [22] compiler_4.1.2         git2r_0.30.1           VEB.Boost_0.0.0.9037  
 [25] cli_3.3.0              rvest_1.0.2            Biobase_2.54.0        
 [28] xml2_1.3.3             labeling_0.4.2         sass_0.4.1            
 [31] scales_1.2.0           mvtnorm_1.1-3          systemfonts_1.0.4     
 [34] digest_0.6.29          spatstat.utils_2.3-1   svglite_2.1.0         
 [37] rmarkdown_2.14         XVector_0.34.0         pkgconfig_2.0.3       
 [40] htmltools_0.5.2        highr_0.9              dbplyr_2.2.0          
 [43] fastmap_1.1.0          rlang_1.0.2            readxl_1.4.0          
 [46] rstudioapi_0.13        RSQLite_2.2.14         farver_2.1.0          
 [49] jquerylib_0.1.4        generics_0.1.2         jsonlite_1.8.0        
 [52] mr.ash.alpha_0.1-42    RCurl_1.98-1.7         magrittr_2.0.3        
 [55] kableExtra_1.3.4       GenomeInfoDbData_1.2.7 Matrix_1.4-1          
 [58] Rcpp_1.0.8.3           munsell_0.5.0          S4Vectors_0.32.4      
 [61] fansi_1.0.3            lifecycle_1.0.1        stringi_1.7.6         
 [64] whisker_0.4            yaml_2.3.5             zlibbioc_1.40.0       
 [67] org.Hs.eg.db_3.14.0    grid_4.1.2             blob_1.2.3            
 [70] parallel_4.1.2         promises_1.2.0.1       crayon_1.5.1          
 [73] lattice_0.20-45        Biostrings_2.62.0      haven_2.5.0           
 [76] hms_1.1.1              KEGGREST_1.34.0        knitr_1.39            
 [79] pillar_1.7.0           stats4_4.1.2           reprex_2.0.1          
 [82] glue_1.6.2             evaluate_0.15          emulator_1.2-21       
 [85] modelr_0.1.8           vctrs_0.4.1            png_0.1-7             
 [88] tzdb_0.3.0             httpuv_1.6.5           cellranger_1.1.0      
 [91] gtable_0.3.0           assertthat_0.2.1       cachem_1.0.6          
 [94] xfun_0.31              broom_0.8.0            later_1.3.0           
 [97] viridisLite_0.4.0      AnnotationDbi_1.56.2   memoise_2.0.1         
[100] IRanges_2.28.0         workflowr_1.7.0        ellipsis_0.3.2

example_yusha_sc_tumor

karltayeb

2022-07-13

Load data

Results

0.fivemg

0.twentymg

0.twentymg2x

0.hundredmg

1.fivemg

1.twentymg

1.twentymg2x

1.hundredmg

2.fivemg

2.twentymg

2.twentymg2x

2.hundredmg

3.fivemg

3.twentymg

3.twentymg2x

3.hundredmg

4.fivemg

4.twentymg

4.twentymg2x

4.hundredmg

5.fivemg

5.twentymg

5.twentymg2x

5.hundredmg

6.fivemg

6.twentymg

6.twentymg2x

6.hundredmg