Visualize and interpret topics in PBMC data
Peter Carbonetto
Last updated: 2020-08-24
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Knit directory: single-cell-topics/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | f7c157a | Peter Carbonetto | 2020-08-24 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| Rmd | e13c17e | Peter Carbonetto | 2020-08-24 | Removed reordering of 68k fit, and fixed downstream PCA analyses. |
| Rmd | 01a0c8b | Peter Carbonetto | 2020-08-24 | Fixed colours in 68k structure plot. |
| html | a0cb7c6 | Peter Carbonetto | 2020-08-24 | Added 68k fit structure plot to plots_pbmc analysis. |
| Rmd | 5b2fb5c | Peter Carbonetto | 2020-08-24 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | b6489db | Peter Carbonetto | 2020-08-23 | Re-built plots_pbmc with new PCA plots from 68k fit. |
| Rmd | 89d98ed | Peter Carbonetto | 2020-08-23 | Removed basic_pca_plot in plots.R; working on PCA plots for 68k fit. |
| html | 13ee038 | Peter Carbonetto | 2020-08-23 | Revised notes in plots_pbmc.Rmd. |
| Rmd | e766da5 | Peter Carbonetto | 2020-08-23 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| Rmd | dbd5882 | Peter Carbonetto | 2020-08-23 | Added some explanatory text to plots_pbmc.Rmd. |
| html | 97d7e86 | Peter Carbonetto | 2020-08-23 | Fixed subclustering of cluster A in purified PBMC data. |
| Rmd | 005b217 | Peter Carbonetto | 2020-08-23 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | 59777e7 | Peter Carbonetto | 2020-08-22 | Added table comparing Zheng et al (2017) labeling with clusters in |
| Rmd | 9cd4a08 | Peter Carbonetto | 2020-08-22 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | c87ddf8 | Peter Carbonetto | 2020-08-22 | Added PBMC purified structure plot with the new clustering (A1, A2, B, |
| Rmd | c6dd5f2 | Peter Carbonetto | 2020-08-22 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | ce421ae | Peter Carbonetto | 2020-08-22 | A few small revisions to plots_pbmc analysis. |
| Rmd | ddc6de4 | Peter Carbonetto | 2020-08-22 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | a406a2f | Peter Carbonetto | 2020-08-22 | Added back first PCA plot for 68k pbmc data. |
| Rmd | 8daa131 | Peter Carbonetto | 2020-08-22 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | 7900d17 | Peter Carbonetto | 2020-08-22 | Revamping the process of defining clusters in plots_pbmc using PCA. |
| Rmd | 14dd774 | Peter Carbonetto | 2020-08-22 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| Rmd | 944ce0c | Peter Carbonetto | 2020-08-22 | Working on new PCA plots for purified PBMC c3 subclusters. |
| html | b05232d | Peter Carbonetto | 2020-08-22 | Build site. |
| Rmd | d0e9f6e | Peter Carbonetto | 2020-08-22 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | fbb0697 | Peter Carbonetto | 2020-08-21 | Build site. |
| Rmd | cdca13e | Peter Carbonetto | 2020-08-21 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | 216027a | Peter Carbonetto | 2020-08-21 | Re-built plots_pbmc webpage with structure plots. |
| Rmd | 98888b2 | Peter Carbonetto | 2020-08-21 | Added structure plots to plots_pbmc.R. |
| html | 9310993 | Peter Carbonetto | 2020-08-21 | Revised the PCA plots in pbmc_plots. |
| Rmd | 3a746ff | Peter Carbonetto | 2020-08-21 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| Rmd | 1091dd0 | Peter Carbonetto | 2020-08-21 | Added code for Ternary plots to plots_pbmc. |
| html | 6d3d7e4 | Peter Carbonetto | 2020-08-20 | Added 68k PCA plots to plots_pbmc. |
| Rmd | 6ec82ca | Peter Carbonetto | 2020-08-20 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | 38f07a2 | Peter Carbonetto | 2020-08-20 | A few small revisions to the plots_pbmc analysis. |
| Rmd | fd0316f | Peter Carbonetto | 2020-08-20 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | 606cd97 | Peter Carbonetto | 2020-08-20 | Added basic PCA plots to plots_pbmc. |
| Rmd | 1b41a60 | Peter Carbonetto | 2020-08-20 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| html | d6e5d39 | Peter Carbonetto | 2020-08-20 | Added PCA plot with purified PBMC clustering to plots_pbmc analysis. |
| Rmd | 99301a7 | Peter Carbonetto | 2020-08-20 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
| Rmd | bf23ca0 | Peter Carbonetto | 2020-08-20 | Added manual labeling of purified PBMC data to plots_pbmc analysis. |
| html | 0c1b570 | Peter Carbonetto | 2020-08-20 | First build on plots_pbmc page. |
| Rmd | eb7f776 | Peter Carbonetto | 2020-08-20 | workflowr::wflow_publish(“plots_pbmc.Rmd”) |
Here we look closely, and compare, the topic modeling results for the two closely related data sets from Zheng et al (2017), the mixture of FACS-purified PBMC data and the “unsorted” 68k PBMC data. The goal is to illustrate how the topic models fitted to these data sets can be used to learn about the structure in the data, identify clusters, and interpret the clusters and topics as “cell types” or “gene programs”.
Load the packages used in the analysis below, as well as additional functions that will be used to generate some of the plots.
library(dplyr)
library(fastTopics)
library(ggplot2)
library(cowplot)
source("../code/plots.R")Mixture of FACS-purified PBMC data
We begin with the mixture of FACS-purified PBMC data. Note that the count data are no longer needed at this stage.
load("../data/pbmc_purified.RData")
samples_purified <- samples
rm(samples,genes,counts)Load the \(k = 6\) Poisson NMF model fit.
fit_purified <-
readRDS("../output/pbmc-purified/rds/fit-pbmc-purified-scd-ex-k=6.rds")$fitHere we explore the structure of the single-cell data as inferred by the topic model. Specifically, we will use PCA to uncover structure in the topic proportions. Although PCA is simple, we will see that it works well, and avoids the complications of the popular t-SNE and UMAP nonlinear dimensionality reduction methods.
fit <- poisson2multinom(fit_purified)
pca <- prcomp(fit$L)$xThree large clusters are evident from first two PCs (there is also finer-scale structure which we will examine below). We label these clusters as “A”, “B” and “C”.
n <- nrow(pca)
x <- rep("C",n)
pc1 <- pca[,"PC1"]
pc2 <- pca[,"PC2"]
x[pc1 + 0.2 > pc2] <- "A"
x[pc2 > 0.25] <- "B"
x[(pc1 + 0.4)^2 + (pc2 + 0.1)^2 < 0.07] <- "C"
samples_purified$cluster <- x
p1 <- pca_plot_with_labels(fit_purified,c("PC1","PC2"),
samples_purified$cluster) +
labs(fill = "cluster")
print(p1)
Most of the samples are in cluster A:
table(x)
# x
# A B C
# 72614 10439 11602Within cluster C there are two fairly well-defined subclusters (labeled “C1” and “C2”). There are perhaps other, less defined subclusters that are less defined, but in this analysis we focus on the largest, most obvious clusters.
rows <- which(samples_purified$cluster == "C")
fit <- select(poisson2multinom(fit_purified),loadings = rows)
pca <- prcomp(fit$L)$x
n <- nrow(pca)
x <- rep("C3",n)
pc1 <- pca[,1]
pc2 <- pca[,2]
x[pc1 < 0 & pc2 < 0.4] <- "C1"
x[pc1 > 0.5 & pc2 < 0.3] <- "C2"
samples_purified[rows,"cluster"] <- x
p2 <- pca_plot_with_labels(fit,c("PC1","PC2"),x) +
labs(fill = "cluster")
print(p2)
| Version | Author | Date |
|---|---|---|
| 7900d17 | Peter Carbonetto | 2020-08-22 |
The two subclusters, C1 and C2, account for most of the samples in cluster C:
table(x)
# x
# C1 C2 C3
# 7822 2990 790Now we turn to cluster A. Within this cluster, there is a large subcluster, which we label as “A1”. (This cluster is much less distinct than the other clusters we have seen so far, and may not show up clearly in this plot—you may need to zoom in on the plot to see the clustering.) Otherwise, there are is obvious additional clustering of the samples within cluster A.
rows <- which(samples_purified$cluster == "A")
fit <- select(poisson2multinom(fit_purified),loadings = rows)
pca <- prcomp(fit$L)$x
n <- nrow(fit$L)
x <- rep("A2",n)
pc1 <- pca[,1]
pc2 <- pca[,2]
x[pc1 > 0.58 - pc2 | pc1 > 0.7] <- "A1"
samples_purified[rows,"cluster"] <- x
p3 <- pca_plot_with_labels(fit,c("PC1","PC2"),x) +
labs(fill = "cluster")
print(p3)
In summary, we have subdivided the data into 6 clusters:
samples_purified$cluster <- factor(samples_purified$cluster)
table(samples_purified$cluster)
#
# A1 A2 B C1 C2 C3
# 8271 64343 10439 7822 2990 790The structure plot provides an evocative visual summary of topic proportions in each of these six clusters:
set.seed(1)
pbmc_purified_topic_colors <- c("gold","forestgreen","dodgerblue",
"gray","greenyellow","magenta")
pbmc_purified_topics <- c(2,5,3,1,4,6)
rows <- sort(c(sample(which(samples_purified$cluster == "A1"),250),
sample(which(samples_purified$cluster == "A2"),1200),
sample(which(samples_purified$cluster == "B"),250),
sample(which(samples_purified$cluster == "C1"),250),
sample(which(samples_purified$cluster == "C2"),200),
sample(which(samples_purified$cluster == "C3"),200)))
p4 <- structure_plot(select(poisson2multinom(fit_purified),loadings = rows),
grouping = samples_purified[rows,"cluster"],
topics = pbmc_purified_topics,
colors = pbmc_purified_topic_colors[pbmc_purified_topics],
gap = 40,num_threads = 4)
print(p4)
# Read the 213 x 6 data matrix successfully!
# OpenMP is working. 4 threads.
# Using no_dims = 1, perplexity = 69.666667, and theta = 0.100000
# Computing input similarities...
# Building tree...
# Done in 0.10 seconds (sparsity = 0.994908)!
# Learning embedding...
# Iteration 50: error is 41.832334 (50 iterations in 0.06 seconds)
# Iteration 100: error is 41.738394 (50 iterations in 0.06 seconds)
# Iteration 150: error is 41.705719 (50 iterations in 0.06 seconds)
# Iteration 200: error is 41.684595 (50 iterations in 0.05 seconds)
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# Iteration 1000: error is 0.127089 (50 iterations in 0.05 seconds)
# Fitting performed in 1.09 seconds.
# Read the 1021 x 6 data matrix successfully!
# OpenMP is working. 4 threads.
# Using no_dims = 1, perplexity = 100.000000, and theta = 0.100000
# Computing input similarities...
# Building tree...
# Done in 0.72 seconds (sparsity = 0.360162)!
# Learning embedding...
# Iteration 50: error is 53.769354 (50 iterations in 0.33 seconds)
# Iteration 100: error is 47.843628 (50 iterations in 0.31 seconds)
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# Fitting performed in 6.43 seconds.
# Read the 213 x 6 data matrix successfully!
# OpenMP is working. 4 threads.
# Using no_dims = 1, perplexity = 69.666667, and theta = 0.100000
# Computing input similarities...
# Building tree...
# Done in 0.07 seconds (sparsity = 0.994908)!
# Learning embedding...
# Iteration 50: error is 42.168186 (50 iterations in 0.06 seconds)
# Iteration 100: error is 41.716690 (50 iterations in 0.06 seconds)
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# Fitting performed in 1.09 seconds.
# Read the 213 x 6 data matrix successfully!
# OpenMP is working. 4 threads.
# Using no_dims = 1, perplexity = 69.666667, and theta = 0.100000
# Computing input similarities...
# Building tree...
# Done in 0.11 seconds (sparsity = 0.994908)!
# Learning embedding...
# Iteration 50: error is 42.127836 (50 iterations in 0.06 seconds)
# Iteration 100: error is 42.139766 (50 iterations in 0.06 seconds)
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# Fitting performed in 1.43 seconds.
# Read the 170 x 6 data matrix successfully!
# OpenMP is working. 4 threads.
# Using no_dims = 1, perplexity = 55.333333, and theta = 0.100000
# Computing input similarities...
# Building tree...
# Done in 0.06 seconds (sparsity = 0.993356)!
# Learning embedding...
# Iteration 50: error is 43.027038 (50 iterations in 0.05 seconds)
# Iteration 100: error is 42.388525 (50 iterations in 0.05 seconds)
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# Fitting performed in 0.86 seconds.
# Read the 170 x 6 data matrix successfully!
# OpenMP is working. 4 threads.
# Using no_dims = 1, perplexity = 55.333333, and theta = 0.100000
# Computing input similarities...
# Building tree...
# Done in 0.06 seconds (sparsity = 0.993218)!
# Learning embedding...
# Iteration 50: error is 43.358844 (50 iterations in 0.05 seconds)
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# Fitting performed in 0.84 seconds.Out of the 6 topics, 4 of them (\(k = 2, 3, 4, 5\)) align closely with the clusters (labeled A1, B, C1, C2). And, indeed, they align closely with their inclusion in the indivvidual FACS-purified data sets:
with(samples_purified,table(celltype,cluster))
# cluster
# celltype A1 A2 B C1 C2 C3
# CD19+ B 0 3 10073 0 1 8
# CD14+ Monocyte 0 30 8 1 2443 130
# CD34+ 4 43 352 7740 545 548
# CD4+ T Helper2 1 11183 0 16 0 13
# CD56+ NK 8243 120 0 17 1 4
# CD8+ Cytotoxic T 21 10135 0 0 0 53
# CD4+/CD45RO+ Memory 0 10201 0 19 0 4
# CD8+/CD45RA+ Naive Cytotoxic 1 11945 3 0 0 4
# CD4+/CD45RA+/CD25- Naive T 1 10440 1 25 0 12
# CD4+/CD25 T Reg 0 10243 2 4 0 14For example, cluster B corresponds almost perfectly to the B-cell data set, and the largest cluster—cluster A2—is comprised of the T-cell data sets. It is also interesting that many of the samples labeled as “CD34+” are not assigned to the CD34+ cluster (C1), which probably reflects the fact that the this population was much less pure (45%) than the others, and so probably contained other cell types.
Cluster C3 is a heterogeneous cluster that we do not investigate further. Cluster A2—see also the PCA plot above—is a clear example where topic modeling is more appropriate than clustering because any additional clustering of the data will be arbitrary.
Unsorted 68k PBMC data
Next, we turn to the 68k data set.
load("../data/pbmc_68k.RData")
samples_68k <- samples
rm(samples,genes,counts)Load the \(k = 6\) Poisson NMF model fit.
fit_68k <- readRDS("../output/pbmc-68k/rds/fit-pbmc-68k-scd-ex-k=6.rds")$fitfit <- poisson2multinom(fit_68k)
pca <- prcomp(fit$L)$xIn this case, we find least three distinct clusters in the projection onto PCs 3 and 4. We label these clusters “A”, “B” and “C”, as above, but this labeling does not imply a connection between the two sets of clusters.
n <- nrow(pca)
x <- rep("A",n)
pc3 <- pca[,"PC3"]
pc4 <- pca[,"PC4"]
x[pc4 < -0.13 | pc3/1.9 - 0.17 > pc4] <- "B"
x[pc4 < -0.75] <- "C"
samples_68k$cluster <- x
p5 <- pca_plot_with_labels(fit_68k,c("PC3","PC4"),x) +
labs(fill = "cluster")
print(p5)
The vast majority of the cells are in cluster A:
table(samples_68k$cluster)
#
# A B C
# 63408 5006 165Looking more closely at cluster B:
rows <- which(samples_68k$cluster == "B")
fit <- select(poisson2multinom(fit_68k),loadings = rows)
pca <- prcomp(fit$L)$x
n <- nrow(pca)
x <- rep("B3",n)
pc1 <- pca[,"PC1"]
x[pc1 > -0.05] <- "B1"
x[pc1 < -0.3] <- "B2"
samples_68k[rows,"cluster"] <- x
p6 <- pca_plot_with_labels(fit,c("PC1","PC2"),x) +
labs(fill = "cluster")
print(p6)
| Version | Author | Date |
|---|---|---|
| b6489db | Peter Carbonetto | 2020-08-23 |
Looking more closely at cluster A:
rows <- which(samples_68k$cluster == "A")
fit <- select(poisson2multinom(fit_68k),loadings = rows)
pca <- prcomp(fit$L)$x
n <- nrow(pca)
x <- rep("A3",n)
pc2 <- pca[,"PC2"]
pc3 <- pca[,"PC3"]
x[2.5*pc3 < 0.3 - pc2] <- "A1"
x[pc3 > 0.8 - pc2] <- "A2"
samples_68k[rows,"cluster"] <- x
p7 <- pca_plot_with_labels(fit,c("PC2","PC3"),x) +
labs(fill = "cluster")
print(p7)
| Version | Author | Date |
|---|---|---|
| b6489db | Peter Carbonetto | 2020-08-23 |
Within cluster A, the vast majority of the samples are assigned to the A1 subcluster:
table(x)
# x
# A1 A2 A3
# 59260 3555 593In summary, we have subdivided these data into 7 clusters:
samples_68k$cluster <- factor(samples_68k$cluster)
table(samples_68k$cluster)
#
# A1 A2 A3 B1 B2 B3 C
# 59260 3555 593 3869 819 318 165TO DO: Add text here.
set.seed(1)
pbmc_68k_topic_colors <- c("gold","lightskyblue","dodgerblue",
"gray","forestgreen","magenta")
pbmc_68k_topics <- c(2,5,1,3,4,6)
rows <- sort(c(sample(which(samples_68k$cluster == "A1"),1200),
sample(which(samples_68k$cluster == "A2"),500),
sample(which(samples_68k$cluster == "A3"),300),
sample(which(samples_68k$cluster == "B1"),500),
sample(which(samples_68k$cluster == "B2"),300),
which(samples_68k$cluster == "B3"),
which(samples_68k$cluster == "C")))
p8 <- structure_plot(select(poisson2multinom(fit_68k),loadings = rows),
grouping = samples_68k[rows,"cluster"],
topics = pbmc_68k_topics,
colors = pbmc_68k_topic_colors[pbmc_68k_topics],
gap = 40,num_threads = 4,verbose = FALSE)
print(p8)
Comparison to Zheng et al (2017) cell-type labeling:
with(samples_68k,table(celltype,cluster))
# cluster
# celltype A1 A2 A3 B1 B2 B3 C
# CD14+ Monocyte 7 0 2 2804 1 46 2
# CD19+ B 1981 3547 342 0 37 1 0
# CD34+ 11 3 49 21 21 9 163
# CD4+ T Helper2 66 0 17 6 8 0 0
# CD4+/CD25 T Reg 6157 0 28 2 0 0 0
# CD4+/CD45RA+/CD25- Naive T 1863 1 4 0 3 2 0
# CD4+/CD45RO+ Memory 3058 0 1 2 0 0 0
# CD56+ NK 8733 0 25 6 1 11 0
# CD8+ Cytotoxic T 20658 1 88 17 0 9 0
# CD8+/CD45RA+ Naive Cytotoxic 16648 0 10 0 5 3 0
# Dendritic 78 3 27 1011 743 237 0
sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.5
#
# 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_1.0.0 ggplot2_3.3.0 fastTopics_0.3-163 dplyr_0.8.3
#
# loaded via a namespace (and not attached):
# [1] ggrepel_0.9.0 Rcpp_1.0.5 lattice_0.20-38
# [4] tidyr_1.0.0 prettyunits_1.1.1 assertthat_0.2.1
# [7] zeallot_0.1.0 rprojroot_1.3-2 digest_0.6.23
# [10] R6_2.4.1 backports_1.1.5 MatrixModels_0.4-1
# [13] evaluate_0.14 coda_0.19-3 httr_1.4.1
# [16] pillar_1.4.3 rlang_0.4.5 progress_1.2.2
# [19] lazyeval_0.2.2 data.table_1.12.8 irlba_2.3.3
# [22] SparseM_1.78 whisker_0.4 Matrix_1.2-18
# [25] rmarkdown_2.3 labeling_0.3 Rtsne_0.15
# [28] stringr_1.4.0 htmlwidgets_1.5.1 munsell_0.5.0
# [31] compiler_3.6.2 httpuv_1.5.2 xfun_0.11
# [34] pkgconfig_2.0.3 mcmc_0.9-6 htmltools_0.4.0
# [37] tidyselect_0.2.5 tibble_2.1.3 workflowr_1.6.2.9000
# [40] quadprog_1.5-8 viridisLite_0.3.0 crayon_1.3.4
# [43] withr_2.1.2 later_1.0.0 MASS_7.3-51.4
# [46] grid_3.6.2 jsonlite_1.6 gtable_0.3.0
# [49] lifecycle_0.1.0 git2r_0.26.1 magrittr_1.5
# [52] scales_1.1.0 RcppParallel_5.0.2 stringi_1.4.3
# [55] farver_2.0.1 fs_1.3.1 promises_1.1.0
# [58] vctrs_0.2.1 tools_3.6.2 glue_1.3.1
# [61] purrr_0.3.3 hms_0.5.2 yaml_2.2.0
# [64] colorspace_1.4-1 plotly_4.9.2 knitr_1.26
# [67] quantreg_5.54 MCMCpack_1.4-5