Chondrocyte CTS and IL1B DE

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Last updated: 2022-07-15

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Knit directory: logistic-susie-gsea/

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File	Version	Author	Date	Message
Rmd	adb077c	karltayeb	2022-07-15	wflow_publish(files = c("analysis/example_anthony.Rmd", "analysis/example_yusha_sc_tumor.Rmd"))
html	ef048c4	karltayeb	2022-07-14	Build site.
Rmd	2dd378e	karltayeb	2022-07-14	wflow_publish("analysis/example_anthony.Rmd")

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Introduction

Anthony differentiated IPSCS -> MSC -> Chondrocytes and treated with physical stress and IL1B.

Load data

source('code/load_data.R')
library(gseasusie)

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

driver = function(gs, experiment){
  dat <- gseasusie::prep_binary_data(gs, data[[experiment]], thresh = 0.05)
  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  <- load_chondrocyte_data2()
go <- gseasusie::load_all_go()
res <- purrr::map(names(data), ~driver_cached('hnscc', go, .x, rerun=F))

#> [1] "hnscc_all_go_CTS.rds"
#> [1] "hnscc_all_go_IL1B.rds"

names(res) <- names(data)

pack_group = function(tbl){
    components <- tbl$component
    unique.components <- unique(components)
    start <- match(unique.components, components)
    end <- c(tail(start, -1) - 1, length(components))
    res <- tbl %>% dplyr::select(-c(component)) %>% kableExtra::kbl()
    for(i in 1:length(unique.components)){
      res <- kableExtra::pack_rows(res, unique.components[i], start[i], end[i])
    }
    return(res)
}

#' Report credible set based summary of SuSiE
#' @export
static_table = function(fit, ora){
  # get credible sets
  res <- gseasusie:::get_gene_set_summary(fit) %>%
    dplyr::left_join(ora)
  csdat <- gseasusie:::get_credible_set_summary(fit) %>%
    dplyr::left_join(ora) %>%
    dplyr::filter(in_cs, active_cs) %>%
    dplyr::select(geneSet, description, component, in_cs, alpha, conditional_beta) %>%
    distinct()
  
  # manipulate table
  columns <- c(
    'geneSet', 'description', 'geneSetSize', 'overlap',
    'log2OR', 'effect', 'alpha', 'pip', 'nlog10pFishersExact', 'fisherRank',
    'component'
  )
  color_columns <- which(columns %in% c('log2OR', 'effect'))
  dt <- res %>% 
    dplyr::filter(overlap > 0) %>%
    dplyr::mutate(
      log2OR = log2(oddsRatio),
      nlog10pFishersExact = -log10(pFishersExact)
    ) %>%
    dplyr::left_join(csdat) %>%
    dplyr::arrange(dplyr::desc(nlog10pFishersExact)) %>%
    dplyr::mutate(
      fisherRank = dplyr::row_number(),
      in_cs = dplyr::if_else(is.na(in_cs), FALSE, in_cs),
      effect = conditional_beta * log2(exp(1))
    ) %>%
    dplyr::filter(in_cs) %>%
    dplyr::select(columns) %>%
    dplyr::mutate(dplyr::across(!where(is.numeric) , as.factor)) %>%
    mutate(
      component = reorder(factor(component), fisherRank, FUN=min) 
      # sorts components
    ) %>%
    dplyr::arrange(component) %>%
    dplyr::mutate_if(is.numeric, funs(as.character(signif(., 3))))

  # display table
  dt %>%
    pack_group %>%
    kableExtra::column_spec(
      color_columns, color=ifelse(dt$effect > 0, 'green', 'red')) %>%
    kableExtra::kable_styling()
}

static_table(fit, ora)

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)
}

CTS

Past versions of results-1.png

Version	Author	Date
ef048c4	karltayeb	2022-07-14

[1] “nothing to report”

IL1B

Past versions of results-2.png

Version	Author	Date
ef048c4	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006952	defense response	710	317	1.22	0.94	1	1	24.8	1
L4
GO:0071944	cell periphery	2460	862	0.729	0.468	0.654	0.654	22.8	2
GO:0005886	plasma membrane	2400	840	0.726	0.465	0.332	0.332	22.3	5
L2
GO:0005634	nucleus	4890	1100	-0.647	-0.527	1	1	22.6	3
L3
GO:0031012	extracellular matrix	280	147	1.63	1.17	0.999	0.999	19.2	18
L5
GO:0009888	tissue development	1110	421	0.813	0.615	0.995	0.995	16.1	33

knitr::knit_exit()