Topic modeling analysis of Buenrostro et al (2018) data with k = 10 topics
Peter Carbonetto
Last updated: 2022-07-11
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Knit directory: scATACseq-topics/
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| File | Version | Author | Date | Message |
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| html | 0493e2f | Peter Carbonetto | 2022-05-10 | Added volcano plots to buenrostro2018_k10 analysis. |
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| html | 63d0c5c | Peter Carbonetto | 2022-05-03 | Improved the structure plot in the buenrostro2018_k10 analysis. |
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Add text here.
Load the packages used in the analysis.
library(Matrix)
library(fastTopics)
library(ggplot2)
library(cowplot)Load the count data, the \(k = 10\) multinomial topic model fit to these data, and the results of the DE analysis using this topic model:
load("data/Buenrostro_2018/processed_data/Buenrostro_2018_binarized.RData")
fit <- readRDS(
file.path("output/Buenrostro_2018/binarized/filtered_peaks",
"fit-Buenrostro2018-binarized-filtered-scd-ex-k=10.rds"))$fit
fit <- poisson2multinom(fit)
load(file.path("output/Buenrostro_2018/binarized/filtered_peaks",
"de-buenrostro2018-k=10-noshrink.RData"))Visualize the structure identified in the FACS cell populations using a Structure plot:
set.seed(1)
celltypes = factor(samples$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")
custom_embed_method <- function (fit, ...) {
y0 <- pca_from_topics(fit,dims = 1)
return(tsne_from_topics(fit,dims = 1,Y_init = matrix(y0),eta = 30,
perplexity = 70,...))
}
structure_plot(fit,grouping = celltypes,n = Inf,gap = 20,
verbose = FALSE,colors = topic_colors,
topics = c(5,10,8,3,4,1,6,7,2,9),
embed_method = custom_embed_method)
The de_analysis function attempts to quantify
differential accessibility in each of the peaks:
n <- nrow(de$z)
k <- ncol(de$z)
p <- vector("list",k)
names(p) <- colnames(de$z)
for (i in 1:k)
p[[i]] <- volcano_plot(de,i,labels = rep("",n)) +
guides(fill = "none")
do.call("plot_grid",c(p,list(nrow = 4,ncol = 3)))
| Version | Author | Date |
|---|---|---|
| 0493e2f | Peter Carbonetto | 2022-05-10 |
The individual results are not strong, but an enrichment analysis of the peaks might point to interesting patterns among these differentially accessible peaks.
sessionInfo()
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