Topic modeling analysis of Cusanovich et al (2018) data with k = 13 topics
Peter Carbonetto
Last updated: 2022-08-01
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Knit directory: scATACseq-topics/
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Add text here summarizing the analysis.
Load the packages used in the analysis below.
library(Matrix)
library(fastTopics)
library(ggplot2)Load the sample meta-data:
tissues <-
c("BoneMarrow_62016","BoneMarrow_62216",
"HeartA_62816","Kidney_62016","Testes_62016","SmallIntestine_62816",
"LargeIntestineA_62816",
"LargeIntestineB_62816","Liver_62016",
"Lung1_62216","Lung2_62216",
"Spleen_62016",
"Thymus_62016","PreFrontalCortex_62216",
"Cerebellum_62216","WholeBrainA_62216","WholeBrainA_62816")
load("data/Cusanovich_2018/processed_data/Cusanovich_2018_metadata_only.RData")
samples <- transform(samples,
tissue.replicate = factor(tissue.replicate,tissues))Next load the \(k = 13\) multinomial topic model fit:
fit <- readRDS("output/Cusanovich_2018/fit-Cusanovich2018-scd-ex-k=13.rds")$fitThis Structure plot shows the cells arranged by tissue. Note that replicates were collected for four of the tissues (bone marrow, lung, small intestine, whole brain) in a second mouse.
set.seed(1)
topic_colors <- c("gold","royalblue","red","sienna","limegreen",
"plum","tomato","purple","cyan","forestgreen",
"darkblue","darkorange","lightgray")
topics <- c(1,2,5,6,9,11,4,10,8,3,7,12,13)
p1 <- structure_plot(fit,grouping = samples$tissue.replicate,gap = 30,n = 4000,
perplexity = 30,colors = topic_colors,topics = topics,
verbose = FALSE)
print(p1)
Reassuringly, the replicates show a very similar distribution of topics. Also reassuringly, some tissues are clearly distinguished by the topics (e.g., thymus), and similar tissues (e.g., small and large intenstine) share topics.
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] ggplot2_3.3.6 fastTopics_0.6-131 Matrix_1.2-18 workflowr_1.7.0
#
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