ps_venn() of phyla overlapped between two groups

[marwa38]

Hello

trying to find the overlapping phyla between two groups (treatments) I know that the total taxa in the phyloseq is 22 while when I am plotting my Venn diagram, I found that they are not 22 in total which is weird Could you please advise on this?

my codes

phylum_glom <- tax_glom(ps.3, taxrank = "Phylum")
# phyloseq-class experiment-level object
# otu_table()   OTU Table:         [ 22 taxa and 35 samples ]
# sample_data() Sample Data:       [ 35 samples by 12 sample variables ]
# tax_table()   Taxonomy Table:    [ 22 taxa by 7 taxonomic ranks ]
# phy_tree()    Phylogenetic Tree: [ 22 tips and 20 internal nodes ]
# refseq()      DNAStringSet:      [ 22 reference sequences ]

ps_venn(phylum_glom, 
        group = "treatment", 
        quantities = list(type="counts", font = 2),
        labels = list(cex = 1),
        main = "ASVs Phyla overlapping by treatment in Stimulus Phase",
        relative = TRUE)

sessionInfo()
# R version 4.1.0 (2021-05-18)
# Platform: x86_64-conda-linux-gnu (64-bit)
# Running under: Ubuntu 20.04.4 LTS
# 
# Matrix products: default
# BLAS/LAPACK: /home/r01mt19/.conda/envs/updatedR/lib/libopenblasp-r0.3.18.so
# 
# locale:
#   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
# [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
# [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
# 
# attached base packages:
#   [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
#   [1] microbiome_1.14.0 ggplot2_3.3.5     phyloseq_1.36.0  
# 
# loaded via a namespace (and not attached):
#   [1] MatrixGenerics_1.4.0        Biobase_2.52.0              tidyr_1.1.4                 jsonlite_1.7.2             
# [5] splines_4.1.0               foreach_1.5.2               RcppParallel_5.1.5          assertthat_0.2.1           
# [9] stats4_4.1.0                latticeExtra_0.6-29         GenomeInfoDbData_1.2.7      Rsamtools_2.8.0            
# [13] yaml_2.2.1                  pillar_1.6.4                lattice_0.20-45             glue_1.6.0                 
# [17] digest_0.6.29               GenomicRanges_1.44.0        RColorBrewer_1.1-2          XVector_0.32.0             
# [21] colorspace_2.0-3            Matrix_1.4-0                plyr_1.8.6                  pkgconfig_2.0.3            
# [25] ShortRead_1.50.0            zlibbioc_1.38.0             purrr_0.3.4                 scales_1.1.1               
# [29] Rtsne_0.15                  jpeg_0.1-9                  BiocParallel_1.26.0         tibble_3.1.6               
# [33] mgcv_1.8-38                 farver_2.1.0                generics_0.1.1              IRanges_2.28.0             
# [37] ellipsis_0.3.2              withr_2.4.3                 SummarizedExperiment_1.22.0 BiocGenerics_0.40.0        
# [41] survival_3.2-13             magrittr_2.0.1              crayon_1.5.0                dada2_1.20.0               
# [45] fansi_0.4.2                 nlme_3.1-153                MASS_7.3-54                 hwriter_1.3.2              
# [49] vegan_2.5-7                 tools_4.1.0                 data.table_1.14.0           lifecycle_1.0.1            
# [53] matrixStats_0.61.0          stringr_1.4.0               Rhdf5lib_1.14.0             S4Vectors_0.32.3           
# [57] munsell_0.5.0               cluster_2.1.2               DelayedArray_0.18.0         Biostrings_2.60.0          
# [61] ade4_1.7-18                 compiler_4.1.0              GenomeInfoDb_1.28.0         rlang_0.4.12               
# [65] rhdf5_2.36.0                grid_4.1.0                  RCurl_1.98-1.5              iterators_1.0.14           
# [69] rhdf5filters_1.4.0          biomformat_1.20.0           rstudioapi_0.13             igraph_1.2.10              
# [73] labeling_0.4.2              bitops_1.0-7                gtable_0.3.0                codetools_0.2-18           
# [77] multtest_2.48.0             DBI_1.1.2                   reshape2_1.4.4              R6_2.5.1                   
# [81] GenomicAlignments_1.28.0    dplyr_1.0.7                 utf8_1.2.2                  permute_0.9-5              
# [85] ape_5.6                     stringi_1.7.6               parallel_4.1.0              Rcpp_1.0.7                 
# [89] vctrs_0.3.8                 png_0.1-7                   tidyselect_1.1.1

phyloseq object attached here: phylum_glom.zip

to read unzip first then phylum_glom <- readRDS(phylum_glom.rds)

[ChiLiubio]

Hi. Sorry. I am not the maintainer of phyloseq package.

[marwa38]

ps_venn() is not from phyloseq package