Last updated: 2022-07-28

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Knit directory: scATACseq-topics/

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File Version Author Date Message
Rmd 2e5bb79 Peter Carbonetto 2022-07-28 workflowr::wflow_publish("analysis/buenrostro2018_k10.Rmd", verbose = TRUE)
html 4efb6dd Peter Carbonetto 2022-07-19 Completed analysis of buenrostro et al topics, with k = 10.
Rmd 21cf91e Peter Carbonetto 2022-07-19 workflowr::wflow_publish("analysis/buenrostro2018_k10.Rmd", verbose = TRUE)
Rmd b520b19 Peter Carbonetto 2022-07-14 Fixed creation of CSV file in buenrostro2018_k10 analysis.
html b520b19 Peter Carbonetto 2022-07-14 Fixed creation of CSV file in buenrostro2018_k10 analysis.
Rmd c318cb4 Peter Carbonetto 2022-07-13 Working on compiling homer results into a table.
html bd4430f Peter Carbonetto 2022-07-13 Build site.
Rmd dcc8027 Peter Carbonetto 2022-07-13 workflowr::wflow_publish("analysis/buenrostro2018_k10.Rmd", verbose = TRUE)
Rmd 287aee7 Peter Carbonetto 2022-07-13 Added some text to the buenrostro2018_k10 analysis and revised the structure plot a bit.
Rmd ebcdcc4 Peter Carbonetto 2022-07-12 In temp.R I have a tile plot I am mostly happy with.
html 8fac509 Peter Carbonetto 2022-07-11 Created exploratory script temp.R.
html 0493e2f Peter Carbonetto 2022-05-10 Added volcano plots to buenrostro2018_k10 analysis.
Rmd a49e37e Peter Carbonetto 2022-05-10 workflowr::wflow_publish("analysis/buenrostro2018_k10.Rmd", verbose = TRUE)
html 63d0c5c Peter Carbonetto 2022-05-03 Improved the structure plot in the buenrostro2018_k10 analysis.
Rmd 2fc232b Peter Carbonetto 2022-05-03 workflowr::wflow_publish("buenrostro2018_k10.Rmd", verbose = TRUE)
Rmd 7853353 Peter Carbonetto 2022-05-03 workflowr::wflow_rename("buenrostro2018_k8.Rmd", "buenrostro2018_k10.Rmd")
html 7853353 Peter Carbonetto 2022-05-03 workflowr::wflow_rename("buenrostro2018_k8.Rmd", "buenrostro2018_k10.Rmd")

Here we summarize and interpret the results from the topic modeling analysis of the Buenrostro et al (2018) data, with \(k = 10\) topics.

Load the packages used in the analysis below.

library(Matrix)
library(fastTopics)
library(ggplot2)
library(cowplot)

Load the count data (see here for details on these data and how they were prepared).

load("data/Buenrostro_2018/processed_data/Buenrostro_2018_binarized.RData")

Next we load the \(k = 10\) multinomial topic model fit to these data, the results of the GoM DE analysis using this topic model, and the results of the HOMER motif enrichment analysis using the p-values from the GoM DE analysis:

fit <- readRDS(
  file.path("output/Buenrostro_2018/binarized/filtered_peaks",
            "fit-Buenrostro2018-binarized-filtered-scd-ex-k=10.rds"))$fit
fit <- poisson2multinom(fit)
load(file.path("output/Buenrostro_2018/binarized/filtered_peaks",
               "de-buenrostro2018-k=10-noshrink.RData"))
homer <- readRDS(file.path("output/Buenrostro_2018/binarized/filtered_peaks",
                           "homer-buenrostro2018-k=10-noshrink.rds"))

Visualize the structure identified in the FACS cell populations using a Structure plot:

set.seed(1)
celltypes <- factor(samples$label,
                    c("pDC","CLP","LMPP","HSC","MPP","CMP","MEP","GMP",
                      "mono","UNK"))
topic_colors <- c("gold","forestgreen","orchid","red","lightgray",
                  "dimgray","orange","dodgerblue","limegreen","mediumblue")
p <- structure_plot(fit,grouping = celltypes,n = Inf,gap = 20,
                     perplexity = 70,verbose = FALSE,colors = topic_colors,
                     topics = c(5,10,8,3,4,1,6,7,2,9))
print(p)

Version Author Date
bd4430f Peter Carbonetto 2022-07-13
8fac509 Peter Carbonetto 2022-07-11
0493e2f Peter Carbonetto 2022-05-10
63d0c5c Peter Carbonetto 2022-05-03
7853353 Peter Carbonetto 2022-05-03

Comparing the topic proportions with the cell labels (provided by FACS), we see that the topics capture chromatin accessibility patterns characteristic of early hematopoietic progenitors (HSC, MPP; topics 2 and 9), and the four different hematopoietic cell lineages: CLPs and LMPPs (topic 8); pDCs (topic 3); monocytes and GMPs (topics 1 and 7); and MEPs (topic 4). Additional topics (topics 5, 6 and 10) may be picking up other factors such as patient-specific batch effects or tissue of origin (bone marrow or blood). Additionally, the split of the HSC/MPP cells into two topics seems to also reflect patient-specific batch effects, which also came up in the PCA analysis in the original paper. We see this more clearly when we arrange the cells by patient id and FACS cell type:

n <- nrow(samples)
x <- rep("unknown",n)
ids <- c("BM4983","BM0106","BM0828","PB1022","BM1077","BM1137","BM1214")
for (id in ids) 
  x[grepl(id,samples$name,fixed = TRUE)] <- id
samples$donor <- factor(x)
set.seed(1)
donor_and_label <- factor(paste(samples$donor,celltypes,sep = "-"))
p <- structure_plot(fit,grouping = donor_and_label,n = Inf,gap = 20,
                     perplexity = 10,verbose = FALSE,colors = topic_colors,
                     topics = c(5,10,8,3,4,1,6,7,2,9))
print(p)

In the GoM DE analysis, we attempt to quantify differential accessibility among topics.

pdat <- data.frame(pval = 10^(-as.vector(de$lpval)))
p <- ggplot(pdat,aes(x = pval)) +
  geom_histogram(bins = 32,color = "white",fill = "black") +
  scale_y_continuous(breaks = seq(0,1e5,2e4)) +
  labs(x = "p-value",y = "LFCs") +
  theme_cowplot(font_size = 10)
print(p)

Version Author Date
4efb6dd Peter Carbonetto 2022-07-19

The issue is that individual regions rarely show significant differences in accessibility, but a motif enrichment analysis of the regions might point to interesting transcription factors common to the more accessible regions. We performed the motif enrichment analysis using HOMER.

First, we compile the motif enrichment p-values into a single table (after removing a small number of duplicate results).

k <- 10
topics <- paste0("k",1:k)
motifs <- sort(unique(homer$k1[,"Motif Name"]))
n <- length(motifs)
homer_lpvals <- matrix(0,n,k)
rownames(homer_lpvals) <- motifs
colnames(homer_lpvals) <- topics
for (i in topics) {
  dat  <- homer[[i]]
  rows <- which(!duplicated(dat[,"Motif Name"]))
  dat  <- dat[rows,]
  rownames(dat)   <- dat[,"Motif Name"]
  homer_lpvals[,i] <- round(dat[motifs,"Log P-value"],digits = 2)
}
dat  <- homer$k1
rows <- which(!duplicated(dat[,"Motif Name"]))
dat  <- dat[rows,]
rownames(dat) <- dat[,"Motif Name"]
homer_lpvals <- cbind(dat[motifs,c("Motif Name","Consensus")],homer_lpvals)

Next, plot the p-values for selected motifs in a tile plot:

# Colors from colorbrewer2.org.
colors <- c("#d73027","#f46d43","#fdae61","#fee090",
            "#e0f3f8","#abd9e9","#74add1","#4575b4")
motifs <- c("Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer",
            "Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer",
            "HOXA1(Homeobox)/mES-Hoxa1-ChIP-Seq(SRP084292)/Homer",
            "ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer",
            "EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer",
            "Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer",
            "Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer",
            "Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer",
            "CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer",
            "CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer",
            "CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer",
            "EBF2(EBF)/BrownAdipose-EBF2-ChIP-Seq(GSE97114)/Homer",
            "EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer",
            "EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer",
            "ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer",
            "GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer",
            "Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer",
            "Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer",
            "GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer",
            "Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer",
            "Gata6(Zf)/HUG1N-GATA6-ChIP-Seq(GSE51936)/Homer",
            "Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer",
            "TCF4(bHLH)/SHSY5Y-TCF4-ChIP-Seq(GSE96915)/Homer",
            "Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer",
            "Fos(bZIP)/TSC-Fos-ChIP-Seq(GSE110950)/Homer",
            "Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer",
            "JunB(bZIP)/DendriticCells-Junb-ChIP-Seq(GSE36099)/Homer")
homer_lpvals <- homer_lpvals[motifs,]
pdat <- NULL
for (i in topics) {
  pdat <- rbind(pdat,
                data.frame(motif = homer_lpvals[,"Motif Name"],
                           topic = i,
                           lpval = homer_lpvals[,i]))
}
pdat <- transform(pdat,
                  topic = factor(topic,c("k9","k2","k3","k4","k8",
                                         "k1","k7","k5","k6","k10")),
            lpval = cut(lpval,c(-Inf,-150,-100,-50,-30,-20,-10,-5,0)),
            motif = factor(motif,rev(motifs)))
p <- ggplot(pdat,aes(x = topic,y = motif,fill = lpval)) +
  geom_tile(color = "white",size = 0.5) +
  scale_fill_manual(values = colors) +
  labs(x = "",y = "") +
  theme_cowplot(font_size = 8)
print(p)

Version Author Date
4efb6dd Peter Carbonetto 2022-07-19

sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] cowplot_1.1.1      ggplot2_3.3.6      fastTopics_0.6-131 Matrix_1.2-18     
# [5] workflowr_1.7.0   
# 
# loaded via a namespace (and not attached):
#  [1] mcmc_0.9-6         fs_1.5.2           progress_1.2.2     httr_1.4.2        
#  [5] rprojroot_1.3-2    tools_3.6.2        backports_1.1.5    bslib_0.3.1       
#  [9] utf8_1.1.4         R6_2.4.1           irlba_2.3.3        uwot_0.1.10       
# [13] DBI_1.1.0          lazyeval_0.2.2     colorspace_1.4-1   withr_2.5.0       
# [17] tidyselect_1.1.1   prettyunits_1.1.1  processx_3.5.2     compiler_3.6.2    
# [21] git2r_0.29.0       quantreg_5.54      SparseM_1.78       plotly_4.9.2      
# [25] labeling_0.3       sass_0.4.0         scales_1.1.0       SQUAREM_2017.10-1 
# [29] quadprog_1.5-8     callr_3.7.0        pbapply_1.5-1      mixsqp_0.3-46     
# [33] systemfonts_1.0.2  stringr_1.4.0      digest_0.6.23      rmarkdown_2.11    
# [37] MCMCpack_1.4-5     pkgconfig_2.0.3    htmltools_0.5.2    fastmap_1.1.0     
# [41] invgamma_1.1       highr_0.8          htmlwidgets_1.5.1  rlang_0.4.11      
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# [49] jsonlite_1.7.2     dplyr_1.0.7        magrittr_2.0.1     Rcpp_1.0.8        
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# [57] whisker_0.4        yaml_2.2.0         MASS_7.3-51.4      Rtsne_0.15        
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# [65] crayon_1.4.1       lattice_0.20-38    hms_1.1.0          knitr_1.37        
# [69] ps_1.6.0           pillar_1.6.2       glue_1.4.2         evaluate_0.14     
# [73] getPass_0.2-2      data.table_1.12.8  RcppParallel_5.1.5 vctrs_0.3.8       
# [77] httpuv_1.5.2       MatrixModels_0.4-1 gtable_0.3.0       purrr_0.3.4       
# [81] tidyr_1.1.3        assertthat_0.2.1   ashr_2.2-54        xfun_0.29         
# [85] coda_0.19-3        later_1.0.0        ragg_0.3.1         viridisLite_0.3.0 
# [89] truncnorm_1.0-8    tibble_3.1.3       ellipsis_0.3.2