Deng et al. Logistic SuSiE GSEA

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Last updated: 2022-04-13

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Overview

We report gene set enrichment analysis of the topics from Jason’s NMF and SNMF of the Deng et al. data set.

For each topic we construct a binary gene list by thresholding on local false sign rates output from flash. Here, I pick \(lfsr <- 1e-5\).

library(tidyverse)
library(htmltools)
source('code/utils.R')

source('code/load_gene_sets.R')
source('code/load_data.R')
data <- load_deng_topics()
genesets <- load_gene_sets()

source('code/logistic_susie_vb.R')
source('code/logistic_susie_veb_boost.R')
source('code/enrichment_pipeline.R')

# fix params
params.genesets <- eval(parse(text=params$genesets))
params.thresh <- eval(parse(text=params$thresh))
params.rerun <- eval(parse(text=params$rerun))

do_logistic_susie_cached = function(data, db, thresh, .sign=c(1, -1), prefix=''){
  res <- xfun::cache_rds({
    purrr::map_dfr(
      names(data),
      ~do_logistic_susie(.x, db, thresh, genesets, data, .sign=.sign))},
    dir = params$cache_dir,
    file=paste0(prefix, 'logistic_susie_', db, '_', thresh),
    hash = list(data, db, thresh, prefix),
    rerun = params.rerun)
}

fits <- map_dfr(params.genesets, ~do_logistic_susie_cached(data, .x, params.thresh))

snmf.data <- data[grep('^SNMF*', names(data))]
positive.fits <- map_dfr(
  params.genesets,
  ~do_logistic_susie_cached(snmf.data, .x, params.thresh, c(1), 'positive_'))

Fitting logistic susie...
    Experiment = SNMF_Topic2
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic3
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic4
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic5
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic6
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic7
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic8
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic9
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic10
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic11
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic12
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic13
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic14
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic15
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic16
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic17
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic18
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic19
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic20
    Database = gobp_nr
    thresh = 1e-04

negative.fits <- map_dfr(
  params.genesets,
  ~do_logistic_susie_cached(snmf.data, .x, params.thresh, c(-1), 'negative_'))

Fitting logistic susie...
    Experiment = SNMF_Topic2
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic3
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic4
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic5
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic6
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic7
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic8
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic9
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic10
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic11
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic12
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic13
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic14
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic15
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic16
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic17
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic18
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic19
    Database = gobp_nr
    thresh = 1e-04Fitting logistic susie...
    Experiment = SNMF_Topic20
    Database = gobp_nr
    thresh = 1e-04

do_ora_cached = function(data, db, thresh, .sign=c(1, -1), prefix=''){
  res <- xfun::cache_rds({
    purrr::map_dfr(names(data), ~do_ora(.x, db, thresh, genesets, data, .sign=.sign))
  },
  dir = params$cache_dir,
  file=paste0(prefix, 'ora_', db, '_', thresh),
  rerun=params.rerun)
}

ora <- map_dfr(params.genesets, ~do_ora_cached(data, .x, params.thresh))
positive.ora <- map_dfr(
  params.genesets,
  ~do_ora_cached(snmf.data, .x, params.thresh, c(1), 'positive_'))
negative.ora <- map_dfr(
  params.genesets,
  ~do_ora_cached(snmf.data, .x, params.thresh, c(-1), 'negative_'))

# take credible set summary, return "best" row for each gene set
get_cs_summary_condensed = function(fit){
  fit %>%
    get_credible_set_summary() %>%
    group_by(geneSet) %>%
    arrange(desc(alpha)) %>%
    filter(row_number() == 1)
}
# generate table for making gene-set plots
get_plot_tbl = function(fits, ora){
  res <- fits %>%
    left_join(ora) %>%
    mutate(
      gs_summary = map(fit, get_gene_set_summary),
      cs_summary = map(fit, get_cs_summary_condensed),
      res = map2(gs_summary, cs_summary, ~ left_join(.x, .y, by='geneSet')),
      res = map2(res, ora, ~ possibly(left_join, NULL)(.x, .y))
    ) %>%
    select(-c(fit, susie.args, ora, gs_summary, cs_summary)) %>%
    unnest(res)
  return(res)
}

# split tibble into a list using 'col'
split_tibble = function(tibble, col = 'col'){
  tibble %>% split(., .[, col])
}
  
# Get summary of credible sets with gene set descriptions
get_table_tbl = function(fits, ora){
  res2 <- fits %>%
    left_join(ora) %>%
    mutate(res = map(fit, get_credible_set_summary)) %>%
    mutate(res = map2(res, ora, ~ left_join(.x, .y))) %>%
    select(-c(fit, ora)) %>%
    unnest(res)

  descriptions <- map_dfr(genesets, ~pluck(.x, 'geneSet', 'geneSetDes'))
  tbl <- res2 %>% 
    filter(active_cs) %>%
    left_join(descriptions)
  tbl_split <- split_tibble(tbl, 'experiment')
  html_tables <- map(tbl_split, ~split_tibble(.x, 'db'))
  return(html_tables)
}

get_ora_enrichments = function(tbl){
   tbl %>% mutate(
    padj = p.adjust(pFishersExact),
    result = case_when(
      padj < 0.05 & oddsRatio < 1 ~ 'depleted',
      padj < 0.05 & oddsRatio > 1 ~ 'enriched',
      TRUE ~ 'not significant'
    )
  )
}

do.volcano = function(res){
  res %>% 
    get_ora_enrichments %>%
    ggplot(aes(x=log10(oddsRatio), y=-log10(pFishersExact), color=result)) +
    geom_point() +
    geom_point(
      res %>% filter(in_cs, active_cs), 
      mapping=aes(x=log10(oddsRatio), y=-log10(pFishersExact)),
      color='black', pch=21, size=5) +
    scale_color_manual(values = c('depleted' = 'coral',
                                  'enriched' = 'dodgerblue',
                                  'not significant' = 'grey'))
}

NMF

Threshold sensitivity

thresh <- map_dbl(1:20, ~10**-.x)

.prop.ones = function(topic){
  map_dbl(thresh, ~ prep_binary_data(
  genesets[['gobp']], data[[topic]], thresh=.x)$y %>% mean())
}

prop.ones <- map_dfc(names(data[grep('^NMF*', names(data))]), ~.prop.ones(.x))

new.names = paste0('Topic', str_pad(2:20, 2, pad='0'))
colnames(prop.ones) <- new.names
prop.ones <- prop.ones %>% mutate(thresh = thresh)

prop.ones %>%
  pivot_longer(one_of(new.names)) %>%
  filter(thresh <= 1e-3) %>%
  group_by(name) %>%
  mutate(value = value / (sort(value, decreasing = T)[1])) %>%
  ggplot(aes(x=-log10(thresh), y=value, color=name)) +
  geom_point() + geom_line() +
  labs(
    y = 'prop.ones relative to 1e-3 threshold',
    title = 'Sensitivity of lfsr to threshold'
  )

Past versions of threshold.sensitivity-1.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13
72fad28	karltayeb	2022-04-09

Glossary

• alpha is the posterior probability of SuSiE including this gene set in this component which is different from PIP (probability of SuSiE including this gene set in ANY component)
• beta posterior mean/standard error of posterior mean for effect size. Standard errors are likely too small.
• oddsRatio, pHypergeometric, pFishersExact construct a contingency table (gene list membersip) x (gene set membership), estimate the oddsRatio gives the odds of being in the gene list conditional on being in the gene set / odds of being in the gene list conditional on NOT being in the gene set. pHypergeometric and pFishersExact are pvalues from 1 and 2 sided test respectively.

res <- fits %>%
  filter(str_detect(experiment, '^NMF*')) %>%
  get_plot_tbl(., ora)

html_tables <- fits %>%
  filter(str_detect(experiment, '^NMF*')) %>%
  get_table_tbl(., ora)

experiments <- unique(res$experiment)

for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  for(db in names(html_tables[[this_experiment]])){
    cat("####", db, "\n") # Create second level headings with the names.
    to_print <- html_tables[[this_experiment]][[db]] %>% distinct()
    to_print %>% report_susie_credible_sets() %>% htmltools::HTML() %>% print()
    cat("\n")
  }}

NMF_Topic2

Past versions of nmf.results-1.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0044772	mitotic cell cycle phase transition	0.97	0.518	0.0949	4.1e-11	7.71e-11	231	435	3.1
GO:0048285	organelle fission	0.0136	0.47	0.102	1.91e-10	3.52e-10	202	376	3.17
GO:1901987	regulation of cell cycle phase transition	0.0052	0.469	0.107	5.79e-08	9.78e-08	176	338	2.95
GO:0007059	chromosome segregation	0.00303	0.52	0.123	3.27e-09	5.82e-09	142	254	3.43
L3
GO:0040029	regulation of gene expression, epigenetic	0.937	0.816	0.137	5e-10	6.8e-10	124	211	3.84
GO:0016458	gene silencing	0.0624	0.853	0.156	6.49e-09	9.52e-09	97	161	4.07
L4
GO:0006399	tRNA metabolic process	0.957	-1.02	0.185	1	3.34e-08	22	136	0.506
GO:0034470	ncRNA processing	0.0394	-0.59	0.118	1	1.43e-06	76	304	0.876
L5
GO:0070646	protein modification by small protein removal	0.954	0.619	0.125	9.91e-08	1.45e-07	135	249	3.19
GO:0000209	protein polyubiquitination	0.0048	0.487	0.131	7.08e-07	1.19e-06	123	229	3.12
GO:0016311	dephosphorylation	0.0015	0.353	0.102	9.77e-06	1.76e-05	187	385	2.56
GO:0016569	covalent chromatin modification	0.00148	0.352	0.101	1.54e-07	2.63e-07	196	387	2.79
GO:0030522	intracellular receptor signaling pathway	0.00138	0.429	0.127	2.37e-05	4.27e-05	124	244	2.78
GO:0140053	mitochondrial gene expression	0.00137	-0.556	0.169	1	1.34e-07	24	139	0.547
GO:0071166	ribonucleoprotein complex localization	0.00127	0.581	0.178	1.03e-05	1.45e-05	68	118	3.63
GO:0009755	hormone-mediated signaling pathway	0.00101	0.467	0.143	3.3e-05	5.5e-05	99	189	2.95
GO:0007265	Ras protein signal transduction	0.000958	0.345	0.103	6.18e-08	1.12e-07	191	372	2.87
GO:0018210	peptidyl-threonine modification	0.000929	0.603	0.192	3.48e-05	4.65e-05	58	100	3.68

NMF_Topic3

Past versions of nmf.results-2.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.85	0.156	5.76e-52	5.76e-52	112	177	13
L10
GO:0070646	protein modification by small protein removal	1	0.922	0.132	3.23e-08	5.52e-08	68	249	2.73
L2
GO:0006414	translational elongation	1	2.67	0.187	2.06e-39	2.06e-39	80	121	14.5
L3
GO:0033108	mitochondrial respiratory chain complex assembly	0.903	2.27	0.262	2.09e-24	2.09e-24	45	64	17.2
GO:0010257	NADH dehydrogenase complex assembly	0.0973	2.59	0.309	8.33e-24	8.33e-24	37	46	29.7
L4
GO:0006605	protein targeting	1	1.2	0.109	1.04e-40	1.04e-40	154	364	5.64
L5
GO:0009123	nucleoside monophosphate metabolic process	0.985	1.2	0.13	2.49e-22	2.49e-22	98	255	4.64
GO:0009141	nucleoside triphosphate metabolic process	0.0145	1.18	0.134	2.16e-23	2.16e-23	97	244	4.9
L6
GO:0022613	ribonucleoprotein complex biogenesis	1	0.96	0.107	7.21e-28	7.21e-28	140	391	4.23
L7
GO:0006457	protein folding	1	1.16	0.154	1.08e-11	1.18e-11	61	179	3.76
L8
GO:0036230	granulocyte activation	0.52	0.798	0.108	7.46e-09	1e-08	96	384	2.44
GO:0002446	neutrophil mediated immunity	0.48	0.796	0.108	9.89e-09	1.65e-08	96	386	2.42
L9
GO:0006399	tRNA metabolic process	1	1.17	0.177	4.79e-08	6.72e-08	44	136	3.44

NMF_Topic4

Past versions of nmf.results-3.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0022613	ribonucleoprotein complex biogenesis	1	1.57	0.111	5.24e-63	8.47e-63	316	391	11.2
L2
GO:0044772	mitotic cell cycle phase transition	1	1.07	0.0979	8.84e-26	1.53e-25	281	435	4.79
L3
GO:0006397	mRNA processing	0.991	1.02	0.102	2.68e-38	3.18e-38	300	425	6.34
L4
GO:0043062	extracellular structure organization	1	-0.871	0.119	1	5.11e-16	63	325	0.593
L5
GO:0016569	covalent chromatin modification	1	0.865	0.103	3.74e-19	5.28e-19	241	387	4.29
L6
GO:0070972	protein localization to endoplasmic reticulum	0.996	1.69	0.191	9.03e-22	1.07e-21	106	131	10.8
L7
GO:0061919	process utilizing autophagic mechanism	1	0.75	0.1	3.83e-11	6.73e-11	226	403	3.3
L8
GO:0034765	regulation of ion transmembrane transport	0.992	-0.865	0.116	1	1.92e-13	73	339	0.678
L9
GO:0098781	ncRNA transcription	0.99	1.7	0.233	1.08e-15	1.74e-15	72	88	11.4
GO:0016073	snRNA metabolic process	0.0101	1.6	0.242	2.81e-16	3.88e-16	67	79	14.1

NMF_Topic5

Past versions of nmf.results-4.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0016197	endosomal transport	0.981	0.86	0.152	1.79e-11	2.92e-11	86	170	3.93
GO:0016482	cytosolic transport	0.016	0.854	0.176	1.24e-08	1.51e-08	64	128	3.82
L2
GO:0061919	process utilizing autophagic mechanism	0.996	0.555	0.0992	7.39e-11	1.21e-10	166	403	2.73
L3
GO:0006091	generation of precursor metabolites and energy	0.989	0.566	0.103	2.31e-07	3.3e-07	143	371	2.43
GO:0009123	nucleoside monophosphate metabolic process	0.00462	0.544	0.125	1.16e-05	2.05e-05	99	255	2.43

NMF_Topic6

Past versions of nmf.results-5.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

NMF_Topic7

Past versions of nmf.results-6.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006397	mRNA processing	0.902	0.985	0.0984	4.02e-22	5.49e-22	275	425	4.59
GO:0008380	RNA splicing	0.0984	1.03	0.106	2.57e-20	3.47e-20	240	367	4.71
L10
GO:0048193	Golgi vesicle transport	1	0.765	0.113	5.69e-10	1.11e-09	185	314	3.53
L2
GO:0034470	ncRNA processing	1	1.09	0.117	2.65e-20	4.71e-20	206	304	5.21
L3
GO:0034765	regulation of ion transmembrane transport	1	-0.961	0.116	1	4.65e-16	72	339	0.638
L4
GO:0061919	process utilizing autophagic mechanism	1	0.757	0.1	2.65e-12	4.95e-12	237	403	3.54
L5
GO:0044772	mitotic cell cycle phase transition	0.987	0.663	0.0971	1.12e-17	2.01e-17	269	435	4.05
GO:0044839	cell cycle G2/M phase transition	0.00606	0.885	0.148	6.1e-15	9.5e-15	129	184	5.73
L6
GO:0031023	microtubule organizing center organization	1	1.36	0.199	5.23e-15	9.82e-15	88	113	8.55
L7
GO:0140053	mitochondrial gene expression	0.999	1.12	0.174	2.21e-11	2.9e-11	97	139	5.61
L8
GO:0006260	DNA replication	0.984	0.877	0.133	2.08e-13	3.72e-13	152	232	4.66
GO:0006289	nucleotide-excision repair	0.00808	1.12	0.194	3.05e-13	5.79e-13	80	104	8.08

NMF_Topic8

Past versions of nmf.results-7.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.59	0.154	1.39e-48	1.39e-48	95	177	12.5
L2
GO:0070972	protein localization to endoplasmic reticulum	1	1.34	0.181	6.8e-38	6.8e-38	72	131	12.9
L3
GO:1990823	response to leukemia inhibitory factor	1	1.55	0.216	1.14e-09	1.14e-09	30	89	5.15
L4
GO:0022613	ribonucleoprotein complex biogenesis	1	0.844	0.108	1.87e-22	1.87e-22	106	391	3.97

NMF_Topic9

Past versions of nmf.results-8.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0002250	adaptive immune response	1	1.19	0.134	8.63e-21	8.63e-21	52	263	6.26
L2
GO:0002521	leukocyte differentiation	1	1.16	0.112	2.84e-22	2.84e-22	66	390	5.3

NMF_Topic10

Past versions of nmf.results-9.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	1.56	0.178	9.82e-25	9.82e-25	86	131	8.35
L2
GO:0022613	ribonucleoprotein complex biogenesis	1	0.886	0.102	3.15e-23	3.83e-23	180	391	3.82
L3
GO:0070646	protein modification by small protein removal	1	0.827	0.126	1.03e-10	1.76e-10	104	249	3.13
L4
GO:0044282	small molecule catabolic process	0.999	-0.69	0.122	1	1.39e-07	41	336	0.582
L5
GO:0034504	protein localization to nucleus	0.954	0.642	0.132	1.81e-07	3.06e-07	88	227	2.74
GO:0006383	transcription by RNA polymerase III	0.00333	0.905	0.276	1.06e-05	1.37e-05	25	47	4.86
GO:0006457	protein folding	0.00246	0.514	0.153	4e-05	5.69e-05	66	179	2.52
GO:0006413	translational initiation	0.00194	0.5	0.152	4.89e-26	4.89e-26	107	177	6.72
GO:0071824	protein-DNA complex subunit organization	0.00188	0.498	0.151	2.59e-07	3.25e-07	73	180	2.95
GO:0016569	covalent chromatin modification	0.0017	0.353	0.105	2.14e-07	3.48e-07	135	387	2.34
GO:0018205	peptidyl-lysine modification	0.00162	0.404	0.122	1.22e-06	1.71e-06	102	283	2.45
GO:0006970	response to osmotic stress	0.000875	0.739	0.259	0.00147	0.00246	24	57	3.1
GO:0040029	regulation of gene expression, epigenetic	0.000865	0.431	0.141	7.41e-06	1.18e-05	78	211	2.53
GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	0.000804	-0.704	0.247	1	1.05e-05	2	64	0.136

NMF_Topic11

Past versions of nmf.results-10.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0034976	response to endoplasmic reticulum stress	1	1.04	0.138	4.45e-10	4.45e-10	51	239	3.33
L2
GO:0002446	neutrophil mediated immunity	0.881	0.859	0.111	1.47e-09	1.95e-09	69	386	2.69
GO:0036230	granulocyte activation	0.119	0.833	0.111	7.16e-09	1.07e-08	67	384	2.61
L3
GO:0070085	glycosylation	0.999	0.893	0.15	2.63e-09	2.63e-09	44	200	3.44
L4
GO:0006643	membrane lipid metabolic process	0.999	0.984	0.167	2.85e-09	2.85e-09	38	159	3.82

NMF_Topic12

Past versions of nmf.results-11.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	1.87	0.181	1.04e-40	1.04e-40	51	131	21
L2
GO:0006413	translational initiation	1	1.72	0.159	4.08e-40	4.08e-40	57	177	15.9

NMF_Topic13

Past versions of nmf.results-12.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	1.88	0.185	1.48e-13	1.48e-13	29	131	7.03

NMF_Topic14

Past versions of nmf.results-13.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	1.38	0.181	3.55e-10	3.55e-10	36	131	4.42
L2
GO:0002446	neutrophil mediated immunity	0.849	0.818	0.111	1.84e-08	2.34e-08	68	386	2.53
GO:0036230	granulocyte activation	0.151	0.795	0.111	7.98e-08	1.08e-07	66	384	2.45

NMF_Topic15

Past versions of nmf.results-14.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

NMF_Topic16

Past versions of nmf.results-15.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

NMF_Topic17

Past versions of nmf.results-16.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0022613	ribonucleoprotein complex biogenesis	1	1.51	0.104	1.45e-48	1.45e-48	154	391	6.39
L10
GO:0009123	nucleoside monophosphate metabolic process	1	1.04	0.133	1.33e-07	1.99e-07	58	255	2.67
L2
GO:0006397	mRNA processing	0.999	0.994	0.101	2.61e-33	2.61e-33	139	425	4.7
L3
GO:0006414	translational elongation	1	1.76	0.185	1.96e-14	1.96e-14	46	121	5.57
L4
GO:0007059	chromosome segregation	1	1.11	0.131	5.27e-15	5.27e-15	74	254	3.79
L5
GO:0070646	protein modification by small protein removal	1	1.14	0.133	2.04e-12	2.1e-12	68	249	3.44
L6
GO:0006260	DNA replication	1	1.01	0.137	1.69e-13	1.69e-13	67	232	3.72
L7
GO:0006457	protein folding	1	1.26	0.156	2.37e-09	2.71e-09	49	179	3.41
L8
GO:0071166	ribonucleoprotein complex localization	0.999	1.23	0.188	3.93e-21	3.93e-21	54	118	7.72
L9
GO:0071824	protein-DNA complex subunit organization	1	1.13	0.155	1.05e-14	1.05e-14	59	180	4.46

NMF_Topic18

Past versions of nmf.results-17.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	2	0.156	1.5e-52	1.5e-52	75	177	17.7
L2
GO:0070972	protein localization to endoplasmic reticulum	1	1.79	0.181	4.58e-47	4.58e-47	62	131	21.1
L3
GO:0009141	nucleoside triphosphate metabolic process	1	1.66	0.14	1.66e-14	1.66e-14	44	244	4.9

NMF_Topic19

Past versions of nmf.results-18.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

NMF_Topic20

Past versions of nmf.results-19.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0002446	neutrophil mediated immunity	0.91	1.33	0.116	2.16e-12	2.16e-12	47	386	3.89
GO:0036230	granulocyte activation	0.0903	1.31	0.117	6.76e-12	6.76e-12	46	384	3.81
L2
GO:0006413	translational initiation	1	1.58	0.167	9.48e-10	9.48e-10	27	177	4.88

SNMF

res <- fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_plot_tbl(., ora)

html_tables <- fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_table_tbl(., ora)

experiments <- unique(res$experiment)
for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  for(db in names(html_tables[[this_experiment]])){
    cat("####", db, "\n") # Create second level headings with the names.
    to_print <- html_tables[[this_experiment]][[db]] %>% distinct()
    to_print %>% report_susie_credible_sets() %>% htmltools::HTML() %>% print()
    cat("\n")
  }}

SNMF_Topic2

Past versions of snmf.results-1.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	0.993	1.21	0.156	1.14e-16	2.15e-16	131	177	6.7

SNMF_Topic3

Past versions of snmf.results-2.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.49	0.153	5.33e-35	5.33e-35	104	177	8.48
L2
GO:0009141	nucleoside triphosphate metabolic process	0.998	0.975	0.13	1.71e-16	2.09e-16	97	244	3.88
L3
GO:0070646	protein modification by small protein removal	1	1.04	0.128	5.44e-13	7.07e-13	91	249	3.38
L4
GO:0070972	protein localization to endoplasmic reticulum	0.992	1.12	0.178	4.78e-27	4.78e-27	78	131	8.65
L5
GO:0010257	NADH dehydrogenase complex assembly	0.976	1.67	0.299	1.18e-13	1.18e-13	31	46	11.9
GO:0033108	mitochondrial respiratory chain complex assembly	0.0234	1.27	0.258	2.2e-11	2.2e-11	35	64	6.94
L6
GO:0006414	translational elongation	0.991	0.962	0.183	1.77e-06	2.95e-06	43	121	3.17

SNMF_Topic4

Past versions of snmf.results-3.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	0.988	1.04	0.15	4.52e-12	5.04e-12	76	177	3.81
GO:0070972	protein localization to endoplasmic reticulum	0.0122	1.11	0.177	3.3e-11	3.67e-11	60	131	4.26

SNMF_Topic5

Past versions of snmf.results-4.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.71	0.151	2.26e-31	2.26e-31	100	177	7.64

SNMF_Topic6

Past versions of snmf.results-5.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0002521	leukocyte differentiation	1	1.19	0.113	9.51e-22	9.51e-22	64	390	5.3
L2
GO:0002250	adaptive immune response	1	1.19	0.135	5.99e-20	5.99e-20	50	263	6.18

SNMF_Topic7

Past versions of snmf.results-6.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0022613	ribonucleoprotein complex biogenesis	1	1.41	0.104	1.63e-71	1.63e-71	236	391	8.45
L10
GO:0098781	ncRNA transcription	0.929	1.25	0.221	4.02e-15	4.02e-15	51	88	7.05
GO:0016073	snRNA metabolic process	0.0509	1.17	0.23	3.94e-13	3.94e-13	45	79	6.75
GO:0006383	transcription by RNA polymerase III	0.0102	1.43	0.304	1.59e-08	1.59e-08	27	47	6.84
L2
GO:0006413	translational initiation	1	1.67	0.156	2.13e-39	2.13e-39	115	177	9.77
L3
GO:0006397	mRNA processing	1	0.965	0.0992	1.03e-42	1.03e-42	208	425	5.21
L4
GO:0070646	protein modification by small protein removal	1	0.983	0.128	5.73e-12	9.41e-12	96	249	3.25
L5
GO:0006360	transcription by RNA polymerase I	0.998	1.72	0.292	4.62e-17	4.62e-17	39	53	14.2
L6
GO:0007059	chromosome segregation	1	0.938	0.128	8.49e-12	9.99e-12	97	254	3.2
L7
GO:0009123	nucleoside monophosphate metabolic process	0.731	0.813	0.128	2.19e-06	3.4e-06	82	255	2.43
GO:0009141	nucleoside triphosphate metabolic process	0.261	0.811	0.131	1.24e-06	2.01e-06	80	244	2.5
L8
GO:0006403	RNA localization	0.99	0.886	0.141	8.39e-26	8.39e-26	110	211	5.7
GO:0051169	nuclear transport	0.00854	0.659	0.12	8.28e-21	9.79e-21	133	310	3.95
L9
GO:0006338	chromatin remodeling	0.962	0.986	0.175	1.73e-10	2.29e-10	59	134	4.03
GO:0006260	DNA replication	0.0117	0.678	0.14	1.84e-09	3.17e-09	85	232	2.98
GO:0071824	protein-DNA complex subunit organization	0.0112	0.748	0.156	5.24e-14	5.54e-14	80	180	4.13
GO:0016569	covalent chromatin modification	0.0065	0.518	0.109	4.55e-11	5.77e-11	131	387	2.67

SNMF_Topic8

Past versions of snmf.results-7.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	0.996	1.08	0.183	2.12e-41	2.12e-41	84	131	14
L2
GO:0022613	ribonucleoprotein complex biogenesis	1	0.881	0.106	1.96e-24	2.03e-24	130	391	3.94
L3
GO:0006414	translational elongation	1	1.52	0.183	3.07e-14	3.07e-14	50	121	5.35
L4
GO:0009141	nucleoside triphosphate metabolic process	0.999	0.979	0.133	4.81e-09	6.22e-09	67	244	2.88
L5
GO:0006413	translational initiation	1	1.12	0.157	3.87e-40	3.87e-40	98	177	9.76
L6
GO:0006605	protein targeting	1	0.865	0.11	6.81e-34	6.81e-34	140	364	5

SNMF_Topic9

Past versions of snmf.results-8.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006401	RNA catabolic process	0.999	0.694	0.114	2.96e-09	4.51e-09	121	304	2.75
L2
GO:0006520	cellular amino acid metabolic process	0.999	0.707	0.125	6.39e-08	8.74e-08	101	254	2.74

SNMF_Topic10

Past versions of snmf.results-9.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	0.962	1.14	0.174	7.35e-10	1.26e-09	55	131	3.91
GO:0090150	establishment of protein localization to membrane	0.0299	0.775	0.128	2.63e-10	3.2e-10	93	266	2.94
L2
GO:0048013	ephrin receptor signaling pathway	0.998	1.26	0.229	2.21e-09	2.21e-09	37	75	5.23
L3
GO:0038127	ERBB signaling pathway	0.971	0.893	0.181	1.02e-07	1.32e-07	48	122	3.49
GO:0070671	response to interleukin-12	0.00272	1.04	0.305	1.28e-05	1.28e-05	21	44	4.88
GO:1990823	response to leukemia inhibitory factor	0.00161	0.737	0.221	1.53e-05	1.71e-05	34	89	3.31
GO:0034109	homotypic cell-cell adhesion	0.00152	0.836	0.255	1.96e-05	2.08e-05	27	65	3.8
GO:0007015	actin filament organization	0.00131	0.404	0.117	6.55e-09	1.05e-08	105	329	2.56
GO:0046847	filopodium assembly	0.00118	0.933	0.296	4.46e-05	4.46e-05	21	47	4.31
GO:0034330	cell junction organization	0.000818	0.442	0.134	1.32e-06	2.33e-06	78	249	2.47
GO:0002446	neutrophil mediated immunity	0.000789	0.362	0.108	1.08e-06	1.6e-06	111	386	2.2
GO:0008544	epidermis development	0.000718	0.433	0.133	1.6e-05	2.3e-05	76	256	2.28
GO:0072337	modified amino acid transport	0.000602	1.16	0.412	0.000954	0.000954	11	22	5.32

SNMF_Topic11

Past versions of snmf.results-10.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic12

Past versions of snmf.results-11.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.4	0.157	1.67e-14	1.67e-14	48	177	4.87
L2
GO:0006414	translational elongation	0.999	1.61	0.187	1.68e-12	1.68e-12	36	121	5.48
L3
GO:0006403	RNA localization	0.998	1.15	0.146	5.16e-12	5.16e-12	49	211	3.95
L4
GO:0071824	protein-DNA complex subunit organization	1	1.2	0.158	1.92e-09	1.92e-09	40	180	3.7

SNMF_Topic13

Past versions of snmf.results-12.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	4.29	0.18	7.55e-52	7.55e-52	40	131	75.8

SNMF_Topic14

Past versions of snmf.results-13.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic15

Past versions of snmf.results-14.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic16

Past versions of snmf.results-15.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic17

Past versions of snmf.results-16.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0034976	response to endoplasmic reticulum stress	1	1.38	0.143	2.37e-11	2.37e-11	39	239	4.22
L2
GO:0002446	neutrophil mediated immunity	0.959	1.14	0.115	6.63e-11	6.63e-11	51	386	3.33
GO:0036230	granulocyte activation	0.0405	1.11	0.116	5.47e-10	5.47e-10	49	384	3.19

SNMF_Topic18

Past versions of snmf.results-17.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic19

Past versions of snmf.results-18.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic20

Past versions of snmf.results-19.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF - Positive loadings

res <- positive.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_plot_tbl(., positive.ora)

html_tables <- positive.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_table_tbl(., positive.ora)

experiments <- unique(res$experiment)
for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  for(db in names(html_tables[[this_experiment]])){
    cat("####", db, "\n") # Create second level headings with the names.
    to_print <- html_tables[[this_experiment]][[db]] %>% distinct()
    to_print %>% report_susie_credible_sets() %>% htmltools::HTML() %>% print()
    cat("\n")
  }}

SNMF_Topic2

Past versions of positive.snmf.results-1.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0022613	ribonucleoprotein complex biogenesis	1	-1.15	0.117	1	7.26e-20	48	391	0.432
L2
GO:0140053	mitochondrial gene expression	1	-1.66	0.206	1	2.62e-12	10	139	0.241
L3
GO:0009123	nucleoside monophosphate metabolic process	0.906	-0.781	0.136	1	1.27e-07	44	255	0.651
GO:0009141	nucleoside triphosphate metabolic process	0.0892	-0.734	0.138	1	6.37e-07	43	244	0.668
L5
GO:0002446	neutrophil mediated immunity	0.803	-0.57	0.108	1	3.48e-06	82	386	0.844
GO:0036230	granulocyte activation	0.192	-0.541	0.109	1	1.27e-05	84	384	0.876

SNMF_Topic3

Past versions of positive.snmf.results-2.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	2.14	0.158	4.42e-57	4.42e-57	90	177	16.6
L2
GO:0010257	NADH dehydrogenase complex assembly	0.998	2.63	0.306	1.9e-25	1.9e-25	31	46	30.6
L3
GO:0070972	protein localization to endoplasmic reticulum	1	1.96	0.184	2.42e-51	2.42e-51	74	131	20.3
L4
GO:0006091	generation of precursor metabolites and energy	1	1.43	0.115	2.58e-27	2.58e-27	91	371	5.11
L5
GO:0006414	translational elongation	1	2.08	0.19	5.8e-15	5.8e-15	37	121	6.53
L6
GO:0070671	response to interleukin-12	1	2.43	0.307	2.64e-11	2.64e-11	19	44	11.1
L7
GO:0002446	neutrophil mediated immunity	0.75	0.987	0.117	1.36e-09	1.53e-09	61	386	2.81
GO:0036230	granulocyte activation	0.25	0.975	0.117	2.91e-09	3.11e-09	60	384	2.77
L8
GO:0070585	protein localization to mitochondrion	1	1.62	0.198	1.38e-09	1.38e-09	29	117	4.83
L9
GO:0043687	post-translational protein modification	1	1.05	0.13	2.38e-06	2.66e-06	45	310	2.5

SNMF_Topic4

Past versions of positive.snmf.results-3.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0016072	rRNA metabolic process	1	0.929	0.141	1.58e-11	2.05e-11	71	210	3.43
L2
GO:0006413	translational initiation	0.998	0.872	0.154	1.54e-09	2.31e-09	59	177	3.34

SNMF_Topic5

Past versions of positive.snmf.results-4.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.38	0.154	1.18e-32	1.18e-32	82	177	8.25
L2
GO:0070972	protein localization to endoplasmic reticulum	1	1.33	0.178	3.96e-30	3.96e-30	67	131	9.9

SNMF_Topic6

Past versions of positive.snmf.results-5.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0002521	leukocyte differentiation	1	1.19	0.115	8.42e-22	8.42e-22	64	390	5.32
L2
GO:0002250	adaptive immune response	1	1.19	0.137	5.43e-20	5.43e-20	50	263	6.2

SNMF_Topic7

Past versions of positive.snmf.results-6.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic8

Past versions of positive.snmf.results-7.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	1.8	0.183	1.74e-45	1.74e-45	83	131	15.8
L2
GO:0006414	translational elongation	1	1.65	0.185	3.5e-16	3.5e-16	49	121	6.05
L3
GO:0022613	ribonucleoprotein complex biogenesis	1	0.866	0.109	6.33e-24	6.33e-24	118	391	4
L4
GO:0010257	NADH dehydrogenase complex assembly	0.983	1.93	0.295	8.01e-09	8.01e-09	21	46	7.32
GO:0033108	mitochondrial respiratory chain complex assembly	0.0174	1.54	0.259	7.55e-08	7.55e-08	24	64	5.24
L5
GO:0006413	translational initiation	1	1.26	0.158	4.36e-43	4.36e-43	95	177	10.7
L6
GO:0070585	protein localization to mitochondrion	1	1.3	0.19	2.14e-08	2.14e-08	36	117	3.9

SNMF_Topic9

Past versions of positive.snmf.results-8.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006302	double-strand break repair	0.996	0.821	0.153	2.03e-07	2.68e-07	64	173	2.96
L2
GO:0006520	cellular amino acid metabolic process	0.994	0.697	0.128	1.89e-07	3.02e-07	86	254	2.59

SNMF_Topic10

Past versions of positive.snmf.results-9.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0007015	actin filament organization	1	0.78	0.115	3.54e-13	4.8e-13	102	329	3.05
L2
GO:0022613	ribonucleoprotein complex biogenesis	1	-1.31	0.132	1	3.1e-12	17	391	0.288
L3
GO:0048013	ephrin receptor signaling pathway	0.999	1.28	0.231	1.34e-10	1.34e-10	35	75	5.79

SNMF_Topic11

Past versions of positive.snmf.results-10.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic12

Past versions of positive.snmf.results-11.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic13

Past versions of positive.snmf.results-12.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic14

Past versions of positive.snmf.results-13.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic15

Past versions of positive.snmf.results-14.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic16

Past versions of positive.snmf.results-15.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic17

Past versions of positive.snmf.results-16.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic18

Past versions of positive.snmf.results-17.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic19

Past versions of positive.snmf.results-18.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic20

Past versions of positive.snmf.results-19.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF - Negative loadings

res <- negative.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_plot_tbl(., negative.ora)

html_tables <- negative.fits %>%
  filter(str_detect(experiment, '^SNMF*')) %>%
  get_table_tbl(., negative.ora)

experiments <- unique(res$experiment)
for (i in 1:length(experiments)){
  this_experiment <- experiments[i]
  cat("\n") 
  cat("###", this_experiment, "\n") # Create second level headings with the names.
  
  # print volcano plot
  p <- do.volcano(res %>% filter(experiment == this_experiment)) +
    labs(title=this_experiment)
  print(p)

  cat("\n\n") 

  # print table
  for(db in names(html_tables[[this_experiment]])){
    cat("####", db, "\n") # Create second level headings with the names.
    to_print <- html_tables[[this_experiment]][[db]] %>% distinct()
    to_print %>% report_susie_credible_sets() %>% htmltools::HTML() %>% print()
    cat("\n")
  }}

SNMF_Topic2

Past versions of negative.snmf.results-1.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.62	0.163	1.49e-58	1.49e-58	110	177	15.3
L10
GO:0006520	cellular amino acid metabolic process	1	0.979	0.136	8.19e-06	1.09e-05	54	254	2.36
L2
GO:0022613	ribonucleoprotein complex biogenesis	1	1.61	0.108	1.24e-53	1.24e-53	163	391	6.86
L3
GO:0006414	translational elongation	1	2.25	0.185	9.03e-27	9.03e-27	62	121	9.38
L4
GO:0010257	NADH dehydrogenase complex assembly	0.912	2.17	0.301	1.3e-17	1.3e-17	30	46	16.4
GO:0033108	mitochondrial respiratory chain complex assembly	0.0881	1.81	0.262	7.73e-17	7.73e-17	35	64	10.6
L5
GO:0070972	protein localization to endoplasmic reticulum	1	1.96	0.19	2.36e-52	2.36e-52	89	131	19.4
L6
GO:0009123	nucleoside monophosphate metabolic process	1	1.11	0.133	1.45e-18	1.45e-18	82	255	4.26
L7
GO:0036230	granulocyte activation	0.528	0.955	0.112	2.86e-09	3.56e-09	85	384	2.53
GO:0002446	neutrophil mediated immunity	0.472	0.952	0.111	3.72e-09	6.04e-09	85	386	2.51
L8
GO:0070585	protein localization to mitochondrion	0.991	1.32	0.193	2.58e-08	2.58e-08	36	117	3.87
L9
GO:0070646	protein modification by small protein removal	1	0.973	0.137	6.59e-08	7.53e-08	59	249	2.73

SNMF_Topic3

Past versions of negative.snmf.results-2.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0051321	meiotic cell cycle	0.998	0.935	0.153	5.46e-08	6.52e-08	46	190	3.09

SNMF_Topic4

Past versions of negative.snmf.results-3.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0072350	tricarboxylic acid metabolic process	1	2.35	0.338	7.25e-09	7.25e-09	13	36	11.7

SNMF_Topic5

Past versions of negative.snmf.results-4.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006414	translational elongation	1	1.38	0.193	1.93e-08	1.93e-08	27	121	4.43

SNMF_Topic6

Past versions of negative.snmf.results-5.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic7

Past versions of negative.snmf.results-6.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0022613	ribonucleoprotein complex biogenesis	1	1.58	0.106	2.03e-80	2.03e-80	232	391	9.4
L10
GO:0006403	RNA localization	0.999	0.926	0.143	3.68e-28	3.68e-28	106	211	6.07
L2
GO:0006397	mRNA processing	1	1.09	0.102	9.02e-48	9.02e-48	201	425	5.64
L3
GO:0006413	translational initiation	1	1.63	0.157	6.03e-39	6.03e-39	108	177	9.45
L4
GO:0071824	protein-DNA complex subunit organization	1	1.07	0.153	1.09e-15	1.82e-15	77	180	4.42
L5
GO:0007059	chromosome segregation	1	0.965	0.13	1.02e-12	1.14e-12	91	254	3.31
L6
GO:0070646	protein modification by small protein removal	1	1.07	0.131	2.71e-13	3.07e-13	91	249	3.42
L7
GO:0010257	NADH dehydrogenase complex assembly	0.927	1.96	0.293	8.37e-08	8.37e-08	24	46	6.32
GO:0033108	mitochondrial respiratory chain complex assembly	0.0723	1.62	0.257	8.19e-07	8.19e-07	28	64	4.51
L8
GO:0098781	ncRNA transcription	0.996	1.46	0.219	5e-16	5e-16	49	88	7.36
L9
GO:0061919	process utilizing autophagic mechanism	1	0.689	0.106	6.65e-07	9.1e-07	109	403	2.19

SNMF_Topic8

Past versions of negative.snmf.results-7.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic9

Past versions of negative.snmf.results-8.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006413	translational initiation	1	1.73	0.163	1.36e-14	1.36e-14	36	177	6.03

SNMF_Topic10

Past versions of negative.snmf.results-9.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	1.78	0.183	8.46e-37	8.46e-37	48	131	18.8
L2
GO:1990823	response to leukemia inhibitory factor	1	2.08	0.229	1.65e-10	1.65e-10	19	89	8.12
L3
GO:0006413	translational initiation	1	1.71	0.161	1.51e-36	1.51e-36	54	177	14.5

SNMF_Topic11

Past versions of negative.snmf.results-10.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic12

Past versions of negative.snmf.results-11.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0006414	translational elongation	1	1.78	0.189	5.07e-15	5.07e-15	36	121	6.7
L2
GO:0022613	ribonucleoprotein complex biogenesis	1	1.1	0.113	2.27e-15	2.27e-15	71	391	3.62
L3
GO:0071824	protein-DNA complex subunit organization	1	1.26	0.162	5.58e-09	5.58e-09	35	180	3.79

SNMF_Topic13

Past versions of negative.snmf.results-12.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0070972	protein localization to endoplasmic reticulum	1	4.8	0.182	3.21e-58	3.21e-58	40	131	127

SNMF_Topic14

Past versions of negative.snmf.results-13.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic15

Past versions of negative.snmf.results-14.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic16

Past versions of negative.snmf.results-15.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic17

Past versions of negative.snmf.results-16.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

gobp_nr

geneSet	description	alpha	beta	beta.se	pHypergeometric	pFishersExact	overlap	geneSetSize	oddsRatio
L1
GO:0034976	response to endoplasmic reticulum stress	1	1.45	0.147	3.72e-11	3.72e-11	34	239	4.58

SNMF_Topic18

Past versions of negative.snmf.results-17.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic19

Past versions of negative.snmf.results-18.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

SNMF_Topic20

Past versions of negative.snmf.results-19.png

Version	Author	Date
a102c2d	karltayeb	2022-04-13

knitr::knit_exit()