NMF analysis of the budding yeast data set
Peter Carbonetto
Last updated: 2025-08-21
Checks: 5 2
Knit directory:
single-cell-jamboree/analysis/
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| Name | Class | Size |
|---|---|---|
| colors | character | 1016 bytes |
| cond_factors | numeric | 112 bytes |
| cond_topics | numeric | 176 bytes |
| conditions | character | 824 bytes |
| counts | dgCMatrix | 333.7 Mb |
| factor_colors | character | 1 Kb |
| fl_nmf_ldf | list | 7.3 Mb |
| genes | data.frame | 2.2 Mb |
| L | matrix;array | 305.1 Kb |
| other_factors | numeric | 112 bytes |
| other_topics | numeric | 96 bytes |
| p1 | gg;ggplot | 327.8 Kb |
| p2 | gg;ggplot | 296.5 Kb |
| rows | integer | 6.3 Kb |
| rows1 | integer | 2.4 Kb |
| rows2 | integer | 4 Kb |
| sample_info | data.frame | 6.3 Mb |
| session_info | sessionInfo | 503.4 Kb |
| timings | list | 2 Kb |
| tm | poisson_nmf_fit;list | 22 Mb |
| topic_colors | character | 1 Kb |
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | dee707e | Peter Carbonetto | 2025-08-21 | Added Structure plots for the topic model in yeast_factors.Rmd. |
| Rmd | 1efebce | Peter Carbonetto | 2025-08-21 | Small edit to yeast_factors.Rmd. |
| Rmd | 58852e7 | Peter Carbonetto | 2025-08-21 | Working on the Structure plots from the NMF analyses of the budding yeast data. |
Load the packages needed for this analysis:
library(Matrix)
library(fastTopics)
library(flashier)
library(singlecelljamboreeR)
library(ggplot2)
library(cowplot)Load the budding yeast data:
load("../data/yeast.RData")Modify the condition labels to match the abbreviations used in the eLife paper:
levels(sample_info$Condition) <-
c("NLIM-NH4","CSTARVE","NLIM-GLN","MMEtOH","MMD","NLIM-PRO",
"NLIM-UREA","YPD","DIAUXY","RAPA","YPEtOH")Reorder the growth conditions in a more logical manner:
conditions <- c("CSTARVE","NLIM-NH4","NLIM-UREA","MMEtOH","NLIM-PRO",
"NLIM-GLN","MMD","YPD","YPEtOH","RAPA","DIAUXY")
sample_info <- transform(sample_info,
Condition = factor(Condition,conditions))Load the results of running fastTopics and flashier on these data:
load("../output/yeast_factors.RData")Topic model (fastTopics)
Structure plots:
topic_colors <-
c("#000000","dodgerblue","darkmagenta","yellow","#FF6800","red",
"olivedrab","gold","greenyellow","#F6768E","darkblue","cornflowerblue",
"navyblue","#B32851","#007D34")
cond_topics <- c(1,2,3,5,7,10,11,4,9)
other_topics <- c(8,12,13,14,15,6)
set.seed(1)
L <- poisson2multinom(tm)$L
rows1 <- which(is.element(sample_info$Condition,c("YPD","RAPA")))
rows2 <- which(!is.element(sample_info$Condition,c("YPD","RAPA")))
rows1 <- sample(rows1,600)
rows2 <- sample(rows2,1000)
rows <- c(rows1,rows2)
L <- L[rows,]
p1 <- structure_plot(L,group = sample_info[rows,"Condition"],
topics = cond_topics,colors = topic_colors,
gap = 10,n = Inf,verbose = FALSE) +
labs(y = "membership")
p2 <- structure_plot(L,group = sample_info[rows,"Condition"],
topics = other_topics,colors = topic_colors,
gap = 10,n = Inf,verbose = FALSE) +
labs(y = "membership")
plot_grid(p1,p2,nrow = 2,ncol = 1)
EBNMF (flashier)
Structure plots:
factor_colors <-
c("#000000","dodgerblue","darkmagenta","yellow","gold","red",
"greenyellow","tomato","olivedrab","#F6768E","darkblue","cornflowerblue",
"navyblue","#B32851","#007D34")
cond_factors <- c(2,3,6,9,10,13,4,1)
other_factors <- c(5,7,8,11,12,14,15)
set.seed(1)
L <- fl_nmf_ldf$L
colnames(L) <- paste0("k",1:15)
rows1 <- which(is.element(sample_info$Condition,c("YPD","RAPA")))
rows2 <- which(!is.element(sample_info$Condition,c("YPD","RAPA")))
rows1 <- sample(rows1,600)
rows2 <- sample(rows2,1000)
rows <- c(rows1,rows2)
L <- L[rows,]
p1 <- structure_plot(L,group = sample_info[rows,"Condition"],
topics = cond_factors,colors = factor_colors,
gap = 10,n = Inf,verbose = FALSE) +
labs(y = "membership")
p2 <- structure_plot(L,group = sample_info[rows,"Condition"],
topics = other_factors,colors = factor_colors,
gap = 10,n = Inf,verbose = FALSE) +
labs(y = "membership")
plot_grid(p1,p2,nrow = 2,ncol = 1)
sessionInfo()
# R version 4.3.3 (2024-02-29)
# Platform: aarch64-apple-darwin20 (64-bit)
# Running under: macOS 15.5
#
# 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] ggplot2_3.5.2 cowplot_1.1.3
# [3] singlecelljamboreeR_0.1-39 flashier_1.0.56
# [5] ebnm_1.1-34 fastTopics_0.7-25
# [7] Matrix_1.6-5 workflowr_1.7.1
#
# loaded via a namespace (and not attached):
# [1] tidyselect_1.2.1 viridisLite_0.4.2 dplyr_1.1.4
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# [46] pbapply_1.7-2 cachem_1.1.0 stringr_1.5.1
# [49] splines_4.3.3 parallel_4.3.3 softImpute_1.4-3
# [52] matrixStats_1.2.0 vctrs_0.6.5 jsonlite_2.0.0
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