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Comparing the Heatmaps for Original and Knockoff Sample Taxa Matrices

We demonstrate the ability of zinck to capture the compositional and highly sparse nature of microbiome count data by comparing the heatmaps of the original sample taxa matrix \(\mathbf{X}\) with its high quality knockoff copy, \(\tilde{\mathbf{X}}\).

We consider a toy setting with \(20\) samples and \(30\) taxa with the library size between \(400\) and \(500\) for each sample, for a high zero-inflation level of \(0.8\). We use the simulateZINLDA() function from the zinLDA package to generate the original sample taxa matrix.

library(zinck)
library(zinLDA)
library(ggplot2)
library(reshape2)
library(gridExtra)
library(cowplot)

set.seed(1) 
N.d=zinLDA::rdu(n=20,min=400,max=500) # Drawing random library sizes between 400, 500
sim_data = zinLDA::simulateZINLDA(D=20,V=30,N=N.d,K=5,Alpha=0.1,Pi=0.8,a=0.5,b=10)
X_original <- sim_data$sampleTaxaMatrix ## The original sample taxa count matrix


model_zinck <- fit.zinck(X_original, num_clusters=5, method="Gibbs", seed=1)
Theta <- model_zinck$theta
Beta <- model_zinck$beta

X_zinck <- generateKnockoff(X_original,Theta,Beta,seed=1)
rownames(X_zinck) <- rownames(X_original)

We will now visualize the heatmaps of the original matrix and its corresponding knockoff copy. The function applies an arcsinh transformation to the data for normalization and better visualization of abundance patterns and zero inflation within the sample taxa matrix.

heat1 <- draw_heatmap(X_original, "Original")
heat2 <- draw_heatmap(X_zinck, "Knockoff")
plot_grid(heat1, heat2, ncol = 2, align="v")

It is evident from the above heatmaps that the knockoff copy is almost indistinguishable from the original matrix! This underscores the fact that the knockoff copy preserves the underlying structure of the observed sample taxa count matrix.


sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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_1.1.1     gridExtra_2.3     reshape2_1.4.4    ggplot2_3.4.2    
[5] zinLDA_0.0.0.9000 zinck_0.0.0.9000  workflowr_1.7.1  

loaded via a namespace (and not attached):
 [1] mcmc_0.9-7           matrixStats_0.63.0   fs_1.6.2            
 [4] httr_1.4.6           rprojroot_2.0.3      rstan_2.21.8        
 [7] tools_4.1.3          bslib_0.5.0          utf8_1.2.3          
[10] R6_2.5.1             DBI_1.1.3            colorspace_2.1-0    
[13] withr_2.5.0          tidyselect_1.2.0     prettyunits_1.1.1   
[16] processx_3.8.1       compiler_4.1.3       git2r_0.32.0        
[19] glmnet_4.1-7         cli_3.6.1            quantreg_5.95       
[22] SparseM_1.81         xml2_1.3.4           NLP_0.2-1           
[25] slam_0.1-50          sass_0.4.6           scales_1.2.1        
[28] tm_0.7-8             randomForest_4.7-1.1 callr_3.7.3         
[31] pbapply_1.7-2        stringr_1.5.0        digest_0.6.31       
[34] StanHeaders_2.21.0-7 rmarkdown_2.22       MCMCpack_1.6-3      
[37] pkgconfig_2.0.3      htmltools_0.5.5      highr_0.10          
[40] fastmap_1.1.1        rlang_1.1.1          rstudioapi_0.14     
[43] shape_1.4.6          jquerylib_0.1.4      generics_0.1.3      
[46] farver_2.1.1         jsonlite_1.8.5       dplyr_1.1.2         
[49] inline_0.3.19        magrittr_2.0.3       modeltools_0.2-23   
[52] loo_2.6.0            Matrix_1.5-1         Rcpp_1.0.10         
[55] munsell_0.5.0        fansi_1.0.4          lifecycle_1.0.3     
[58] stringi_1.7.12       whisker_0.4.1        yaml_2.3.7          
[61] MASS_7.3-60          pkgbuild_1.4.2       plyr_1.8.8          
[64] grid_4.1.3           parallel_4.1.3       promises_1.2.0.1    
[67] crayon_1.5.2         lattice_0.21-8       splines_4.1.3       
[70] knockoff_0.3.6       knitr_1.43           ps_1.7.5            
[73] pillar_1.9.0         topicmodels_0.2-14   codetools_0.2-19    
[76] stats4_4.1.3         glue_1.6.2           evaluate_0.21       
[79] getPass_0.2-2        RcppParallel_5.1.7   vctrs_0.6.5         
[82] httpuv_1.6.11        foreach_1.5.2        MatrixModels_0.5-1  
[85] gtable_0.3.3         cachem_1.0.8         xfun_0.39           
[88] coda_0.19-4          later_1.3.1          survival_3.5-5      
[91] tibble_3.2.1         iterators_1.0.14