Last updated: 2024-12-12

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This goal of this analysis is to apply Neighbor joining to different matrix factorization approaches to the pancreas data set and assess how well it works for this data set.

First, load the packages needed for this analysis.

library(Matrix)
library(fastTopics)
# Warning: package 'fastTopics' was built under R version 4.4.2
library(ggplot2)
library(cowplot)
library(ape)
# Warning: package 'ape' was built under R version 4.4.2

Set the seed for reproducibility.

set.seed(1)

This is a function I will use below to subsample the cell types that have a lot of cells so that the rare cell types are more visible in the Structure plots.

subsample_cell_types <- function (x, n = 1000) {
  cells <- NULL
  groups <- levels(x)
  for (g in groups) {
    i  <-  which(x == g)
    n0 <- min(n,length(i))
    i  <- sample(i,n0)
    cells <- c(cells,i)
  }
  return(sort(cells))
}

Load the pancreas data set and the outputs generated from running the compute_pancreas_factors.R and compute_pancreas_factors2.R scripts.

load("../data/pancreas.RData")
load("../output/pancreas_factors.RData")
timings0 <- timings
load("../output/pancreas_factors2.RData")
timings <- c(timings0,timings)

flashier NMF

Reproduction of Peter resulst

cells <- subsample_cell_types(sample_info$celltype,n = 500)
L <- fl_nmf_ldf$L
k <- ncol(L)
colnames(L) <- paste0("k",1:k)
batch_factors    <- c(2:5,7:8,20)
celltype_factors <- c(6,11:19,21)
other_factors    <- c(1,9:10,22:23)
celltype <- sample_info$celltype
celltype <-
 factor(celltype,
        c("acinar","ductal","activated_stellate","quiescent_stellate",
          "endothelial","macrophage","mast","schwann","t_cell","alpha",
          "beta","delta","gamma","epsilon"))
p1 <- structure_plot(L,topics = batch_factors,grouping = sample_info$tech,
                     gap = 10,perplexity = 70) +
  labs(y = "membership",title = "data-set factors",
       fill = "factor",color = "factor")
p2 <- structure_plot(L[cells,],topics = celltype_factors,
                     grouping = celltype[cells],gap = 25,
                     n = Inf,perplexity = 70) +
  labs(y = "membership",title = "cell-type factors",
       fill = "factor",color = "factor")
p3 <- structure_plot(L[cells,],topics = other_factors,
                     grouping = celltype[cells],gap = 25,
                     n = Inf,perplexity = 70) +
  labs(y = "membership",title = "other factors",
       fill = "factor",color = "factor")
plot_grid(p1,p2,p3,nrow = 3,ncol = 1)

Let’s start by applying NJ to all the factor together. It generates a couple of negative edge length that we correct


dist_mat= t(fl_nmf_ldf$F)%*%fl_nmf_ldf$F
dimnames(dist_mat)= list(1:ncol(dist_mat), 1:ncol(dist_mat))
check_tree=nj(dist_mat )
plot(check_tree, main="NMF +NJ")

check_tree$edge.length=abs(check_tree$edge.length)
plot(check_tree)

Lets now focus just on the so called celltype_factors and apply NJ

celltype_factors <-c(6,11:19,21)

check_tree=nj(dist_mat[celltype_factors, celltype_factors] )
plot(check_tree, main="Cell factor + NMF +NJ")

check_tree$edge.length=abs(check_tree$edge.length)
check_tree
plot(check_tree)

# 
# Phylogenetic tree with 11 tips and 9 internal nodes.
# 
# Tip labels:
#   6, 11, 12, 13, 14, 15, ...
# 
# Unrooted; includes branch lengths.

In this case there are no negative edge

Note that factors that are close on the tree tend not to appear together in the “factor plot” above (eg. 11 and 6 or 14 and 15)

In other words if a cell is loaded in one of the branch it tends not to be loaded in a branch within its vicinity.

Topic model (fastTopics)

Peter script

L <- poisson2multinom(pnmf)$L
batch_topics     <- c(2,5,6,11,12)
celltype_topics  <- c(4,9,8,15,16,17,18,19,20)
celltype_topics2 <- c(1,3,7,10,13,14,21,22,23)
p1 <- structure_plot(L[,batch_topics],grouping = sample_info[,"tech"],
                     gap = 10,perplexity = 70) +
  ggtitle("data-set topics")
p2 <- structure_plot(L[cells,celltype_topics],grouping = celltype[cells],
                     gap = 25,perplexity = 70,n = Inf) +
  ggtitle("cell-type topics")                    
p3 <- structure_plot(L[cells,celltype_topics2],grouping = celltype[cells],
                     gap = 25,perplexity = 70,n = Inf) +
  ggtitle("more cell-type topics")                   
plot_grid(p1,p2,p3,nrow = 3,ncol = 1)

Same let’s run NJ on all the factor and then let’s focus of the cell topic

dist_mat=  t(pnmf$F)%*% pnmf$F
dimnames(dist_mat)= list(1:ncol(dist_mat), 1:ncol(dist_mat))
check_tree=nj(dist_mat   )
 
plot(check_tree, main="Topic +NJ")

check_tree$edge.length=abs(check_tree$edge.length)
check_tree
plot(check_tree)

# 
# Phylogenetic tree with 23 tips and 21 internal nodes.
# 
# Tip labels:
#   1, 2, 3, 4, 5, 6, ...
# 
# Unrooted; includes branch lengths.

Clearly the tree do not make sens. Let’s look at the celltopic only


check_tree=nj( dist_mat[celltype_topics, celltype_topics]    )
 
plot(check_tree, main="Cell topic + FastTopic +NJ")

check_tree$edge.length=abs(check_tree$edge.length)
check_tree
plot(check_tree)

# 
# Phylogenetic tree with 9 tips and 7 internal nodes.
# 
# Tip labels:
#   4, 9, 8, 15, 16, 17, ...
# 
# Unrooted; includes branch lengths.

Unfortunately this tree still has some problem. However we notice the same pattern as before. What is close on the tree tend not to co-occur on the “factor plot” In other words if a cell is loaded in one of the branch it tend not to be loaded in a branch within its vicinity. (eg 4 and 9 or 18 and 19)


sessionInfo()
# R version 4.4.1 (2024-06-14 ucrt)
# Platform: x86_64-w64-mingw32/x64
# Running under: Windows 11 x64 (build 22631)
# 
# Matrix products: default
# 
# 
# locale:
# [1] LC_COLLATE=English_United States.utf8 
# [2] LC_CTYPE=English_United States.utf8   
# [3] LC_MONETARY=English_United States.utf8
# [4] LC_NUMERIC=C                          
# [5] LC_TIME=English_United States.utf8    
# 
# time zone: Europe/Oslo
# tzcode source: internal
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] ape_5.8            cowplot_1.1.3      ggplot2_3.5.1      fastTopics_0.6-192
# [5] Matrix_1.7-0      
# 
# loaded via a namespace (and not attached):
#  [1] gtable_0.3.6        xfun_0.49           bslib_0.8.0        
#  [4] htmlwidgets_1.6.4   ggrepel_0.9.6       lattice_0.22-6     
#  [7] quadprog_1.5-8      vctrs_0.6.5         tools_4.4.1        
# [10] generics_0.1.3      parallel_4.4.1      tibble_3.2.1       
# [13] fansi_1.0.6         pkgconfig_2.0.3     data.table_1.16.2  
# [16] SQUAREM_2021.1      RcppParallel_5.1.9  lifecycle_1.0.4    
# [19] truncnorm_1.0-9     farver_2.1.2        compiler_4.4.1     
# [22] stringr_1.5.1       git2r_0.35.0        progress_1.2.3     
# [25] munsell_0.5.1       RhpcBLASctl_0.23-42 httpuv_1.6.15      
# [28] htmltools_0.5.8.1   sass_0.4.9          yaml_2.3.10        
# [31] lazyeval_0.2.2      plotly_4.10.4       crayon_1.5.3       
# [34] later_1.4.1         pillar_1.9.0        jquerylib_0.1.4    
# [37] whisker_0.4.1       tidyr_1.3.1         uwot_0.2.2         
# [40] cachem_1.1.0        nlme_3.1-164        gtools_3.9.5       
# [43] tidyselect_1.2.1    digest_0.6.37       Rtsne_0.17         
# [46] stringi_1.8.4       dplyr_1.1.4         purrr_1.0.2        
# [49] ashr_2.2-63         labeling_0.4.3      rprojroot_2.0.4    
# [52] fastmap_1.2.0       grid_4.4.1          colorspace_2.1-1   
# [55] cli_3.6.3           invgamma_1.1        magrittr_2.0.3     
# [58] utf8_1.2.4          withr_3.0.2         prettyunits_1.2.0  
# [61] scales_1.3.0        promises_1.3.2      rmarkdown_2.29     
# [64] httr_1.4.7          workflowr_1.7.1     hms_1.1.3          
# [67] pbapply_1.7-2       evaluate_1.0.1      knitr_1.49         
# [70] viridisLite_0.4.2   irlba_2.3.5.1       rlang_1.1.4        
# [73] Rcpp_1.0.13         mixsqp_0.3-54       glue_1.7.0         
# [76] rstudioapi_0.17.1   jsonlite_1.8.8      R6_2.5.1           
# [79] fs_1.6.5