Examine topic modeling results with k = 16 topics
Peter Carbonetto
Last updated: 2025-05-19
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Knit directory: lps/analysis/
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| File | Version | Author | Date | Message |
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| Rmd | 6425fe5 | Peter Carbonetto | 2025-05-19 | wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE, |
| html | 9512227 | Peter Carbonetto | 2025-05-19 | Ran wflow_publish("examine_topic_model_k16.Rmd") |
| Rmd | 81bea77 | Peter Carbonetto | 2025-05-19 | wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE, |
| Rmd | 6419ec8 | Peter Carbonetto | 2022-06-14 | Created PDF containing single-topic structure plots. |
| Rmd | a584893 | Peter Carbonetto | 2022-06-14 | Removed a file that is not needed. |
| Rmd | 6b2ab80 | Peter Carbonetto | 2022-06-13 | Added metadata csv file; implemented script check_outlier.R. |
| Rmd | 0428e4c | Peter Carbonetto | 2022-06-02 | Added some code to create a PDF of the main structure plot in the examine_topic_model_k16 analysis. |
| Rmd | abc3e45 | Peter Carbonetto | 2022-05-19 | A few small fixes to the examine_topic_model_k16 analysis. |
| html | abc3e45 | Peter Carbonetto | 2022-05-19 | A few small fixes to the examine_topic_model_k16 analysis. |
| html | 2e949c0 | Peter Carbonetto | 2022-05-10 | Added links to volcano plots. |
| Rmd | ba08036 | Peter Carbonetto | 2022-05-10 | workflowr::wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE) |
| html | 29047dc | Peter Carbonetto | 2022-05-10 | Build site. |
| Rmd | 23fcc2b | Peter Carbonetto | 2022-05-10 | workflowr::wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE) |
| html | 6e95930 | Peter Carbonetto | 2022-05-10 | Fixed interactive volcano_plots. |
| Rmd | a136de3 | Peter Carbonetto | 2022-05-10 | workflowr::wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE) |
| html | bef8deb | Peter Carbonetto | 2022-05-10 | Added volcano plots. |
| Rmd | 567870b | Peter Carbonetto | 2022-05-10 | workflowr::wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE) |
| html | 6dabc4d | Peter Carbonetto | 2022-05-05 | Added another structure plot to examine_topic_model_k16 analysis. |
| Rmd | 1899304 | Peter Carbonetto | 2022-05-05 | workflowr::wflow_publish("examine_topic_model_k16.Rmd") |
| html | b5a1eae | Peter Carbonetto | 2022-05-04 | Build site. |
| Rmd | a628c54 | Peter Carbonetto | 2022-05-04 | workflowr::wflow_publish("examine_topic_model_k16.Rmd", verbose = TRUE) |
| Rmd | e01a993 | Peter Carbonetto | 2022-05-04 | First build of overview page. |
Load the packages used in the analysis.
library(data.table)
library(fastTopics)
library(ggplot2)
library(cowplot)
source("../code/lps_data.R")Initialize the sequence of pseudorandom numbers.
set.seed(1)Load the count data.
dat <- read_lps_data("../data/raw_read_counts.csv.gz")
samples <- dat$samples
counts <- dat$counts
table(samples$tissue)
table(samples$timepoint)
table(samples$mouse)
#
# BM BR CO HE iLN KI LI LU PBMC SI SK SP TH
# 28 28 28 28 28 28 28 28 28 28 28 28 28
#
# d0 d0.25 d0.5 d1 d2 d3 d5
# 52 52 52 52 52 52 52
#
# 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 3 4 5 6 7
# 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
# 8 9
# 13 13Remove genes with very low (or no) expression.
j <- which(colSums(counts) > 20)
counts <- counts[,j]Load the results of the topic modeling analysis.
load("../output/fit-lps-k=16.RData")Plot the improvement in the solution over time.
p1 <- plot_progress(fit,x = "timing",y = "loglik",colors = "black",
add.point.every = 10,e = 1e-4) +
guides(color = "none",fill = "none",shape = "none",
linetype = "none",size = "none")
p2 <- plot_progress(fit,x = "timing",y = "res",colors = "black",
add.point.every = 10,e = 1e-4) +
guides(color = "none",fill = "none",shape = "none",
linetype = "none",size = "none")
plot_grid(p1,p2)
Visualize the structure identified in each of the tissues using a Structure plot, in which the samples in each tissue are ordered by time in which the sample was taken:
set.seed(1)
rows <- order(samples$timepoint)
topic_colors <- c("darkblue","dodgerblue","darkorange","forestgreen",
"limegreen","tomato","darkred","olivedrab","magenta",
"darkmagenta","sienna","royalblue","lightskyblue",
"gold","red","cyan")
p <- structure_plot(fit,grouping = samples$tissue,gap = 5,
colors = topic_colors,
topics = c(15,3,4,5,6,7,8,9,10,11,12,13,2,14,1,16),
loadings_order = rows) +
theme(legend.key.height = unit(0.15,"cm"),
legend.text = element_text(size = 7))
print(p)
See here for more Structure plots.
There is a single topic (topic 9, blue in the plot below) that is capturing changes in expression over time across many tissues. Two other topics (topics 1 and 6) show similar patterns, except these patterns are specific to two tissues (PBMC and LI).
set.seed(1)
topic_colors <- c("gold","darkorange","dodgerblue","white")
fit2 <- poisson2multinom(fit)
fit2 <- merge_topics(fit2,paste0("k",setdiff(1:16,c(1,6,9))))
colnames(fit2$L) <- c("k1","k6","k9","other")
p <- structure_plot(fit2,grouping = samples$tissue,gap = 5,
colors = topic_colors,topics = c(4,1:3),
loadings_order = rows)
print(p)
These volcano plots summarize the results of the DE analysis for topics capturing different tissues (and topic 9, which is capturing changes in expression at different time points):
topics <- colnames(de_merged$z)
p <- vector("list",13)
names(p) <- topics
for (k in topics) {
p[[k]] <- volcano_plot(de_merged,k = k,ymax = 500) +
guides(color = "none")
volcano_plotly(de_merged,k = k,ymax = 500,
file = paste("volcano_plot_",k,".html",sep = ""))
}
do.call("plot_grid",c(p,list(ncol = 3,nrow = 5)))
These volcano plots summarize the results of the DE analysis for topics capturing expression patterns within tissues:
topics <- c("k1","k2","k5","k6","k13","k14")
p <- vector("list",6)
names(p) <- topics
for (k in topics) {
p[[k]] <- volcano_plot(de,k = k,ymax = 300) +
guides(color = "none")
volcano_plotly(de,k = k,ymax = 300,
file = paste("volcano_plot_",k,".html",sep = ""))
}
do.call("plot_grid",c(p,list(ncol = 3,nrow = 2)))
These results may also be browsed interactively: k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13, k14, k15, k16, k1+k5, k2+k13, k6+k14.
sessionInfo()
# R version 4.3.3 (2024-02-29)
# Platform: aarch64-apple-darwin20 (64-bit)
# Running under: macOS 15.4.1
#
# Matrix products: default
# BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#
# time zone: America/Chicago
# tzcode source: internal
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] cowplot_1.1.3 ggplot2_3.5.0 fastTopics_0.7-24 data.table_1.15.2
#
# loaded via a namespace (and not attached):
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# [13] tibble_3.2.1 fansi_1.0.6 highr_0.10
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