Last updated: 2022-08-01

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Knit directory: scATACseq-topics/

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    Ignored:    output/Buenrostro_2018/binarized/filtered_peaks/fit-Buenrostro2018-binarized-filtered-scd-ex-k=10.rds
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    Untracked:  output/Cusanovich_2018/
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Rmd db1e9f0 Peter Carbonetto 2022-08-01 workflowr::wflow_publish("analysis/cusanovich2018_k13.Rmd", verbose = TRUE)
html 52d4663 Peter Carbonetto 2022-08-01 First build of cusanovich2018_k13 analysis.
Rmd cf89aa8 Peter Carbonetto 2022-08-01 workflowr::wflow_publish("analysis/cusanovich2018_k13.Rmd", verbose = TRUE)

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")$fit

Add text here.

set.seed(1)
topic_colors <- c("royalblue","gold","red","sienna","limegreen",
                  "plum","tomato","purple","dodgerblue","forestgreen",
                  "darkblue","darkorange","lightskyblue")
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)

Version Author Date
52d4663 Peter Carbonetto 2022-08-01 

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   
# 
# loaded via a namespace (and not attached):
#  [1] mcmc_0.9-6         fs_1.5.2           progress_1.2.2     httr_1.4.2        
#  [5] rprojroot_1.3-2    tools_3.6.2        backports_1.1.5    bslib_0.3.1       
#  [9] utf8_1.1.4         R6_2.4.1           irlba_2.3.3        uwot_0.1.10       
# [13] DBI_1.1.0          lazyeval_0.2.2     colorspace_1.4-1   withr_2.5.0       
# [17] tidyselect_1.1.1   prettyunits_1.1.1  processx_3.5.2     compiler_3.6.2    
# [21] git2r_0.29.0       quantreg_5.54      SparseM_1.78       plotly_4.9.2      
# [25] labeling_0.3       sass_0.4.0         scales_1.1.0       SQUAREM_2017.10-1 
# [29] quadprog_1.5-8     callr_3.7.0        pbapply_1.5-1      mixsqp_0.3-46     
# [33] systemfonts_1.0.2  stringr_1.4.0      digest_0.6.23      rmarkdown_2.11    
# [37] MCMCpack_1.4-5     pkgconfig_2.0.3    htmltools_0.5.2    fastmap_1.1.0     
# [41] invgamma_1.1       highr_0.8          htmlwidgets_1.5.1  rlang_0.4.11      
# [45] rstudioapi_0.13    jquerylib_0.1.4    generics_0.0.2     farver_2.0.1      
# [49] jsonlite_1.7.2     dplyr_1.0.7        magrittr_2.0.1     Rcpp_1.0.8        
# [53] munsell_0.5.0      fansi_0.4.0        lifecycle_1.0.0    stringi_1.4.3     
# [57] whisker_0.4        yaml_2.2.0         MASS_7.3-51.4      Rtsne_0.15        
# [61] grid_3.6.2         parallel_3.6.2     promises_1.1.0     ggrepel_0.9.1     
# [65] crayon_1.4.1       lattice_0.20-38    cowplot_1.1.1      hms_1.1.0         
# [69] knitr_1.37         ps_1.6.0           pillar_1.6.2       glue_1.4.2        
# [73] evaluate_0.14      getPass_0.2-2      data.table_1.12.8  RcppParallel_5.1.5
# [77] vctrs_0.3.8        httpuv_1.5.2       MatrixModels_0.4-1 gtable_0.3.0      
# [81] purrr_0.3.4        tidyr_1.1.3        assertthat_0.2.1   ashr_2.2-54       
# [85] xfun_0.29          coda_0.19-3        later_1.0.0        ragg_0.3.1        
# [89] viridisLite_0.3.0  truncnorm_1.0-8    tibble_3.1.3       ellipsis_0.3.2