search

ChiLiubio / microeco

An R package for data analysis in microbial community ecology
GNU General Public License v3.0
195 stars 56 forks source link

Taxa labels dont show up after performing plot_diff_cladogram #367

Closed BiggusDickus666 closed 4 months ago

BiggusDickus666 commented 4 months ago

Hi, I have recently performed the representation of differential abundance analysis as a cladogram following Microeco guide. I noticed that taxa names do not appear in the cladogram. What may be causing the problem? Here you can find attached the cladogram

Thank you very much in advance!!

diffMicroecoTripIno.pdf

ChiLiubio commented 4 months ago

Hi. Please attach your microtable data and steps so that I can reproduce your issue? To save the dataset, please follow the steps in the tutorial (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function) and attach the compressed object. I will have a try.

BiggusDickus666 commented 4 months ago

Hi @ChiLiubio , Here you can find attached my microtable object. Thank you very much for your help!!

[Uploading MicroecoIno.zip…]()

ChiLiubio commented 4 months ago

Hi. The link can not be opened. Please make sure it is available. Please also provide the R script.

BiggusDickus666 commented 4 months ago

Hi @ChiLiubio Sorry for that, hope this link work! Thanks for your patience MicroecoIno.zip

BiggusDickus666 commented 4 months ago

And here it is the R script:

Importing .qza from QIIME2 for microtable object construction

table_microecoTriplicates<- "/home/victor/Escritorio/Microeco/merged-table.qza" rep_microecoTriplicates<- "/home/victor/Escritorio/Microeco/rep-seqs.qza" taxonomy_microecoTriplicates<- "/home/victor/Escritorio/Microeco/microecotaxonomy.qza" tree_microecoTriplicates<- "/home/victor/Escritorio/Microeco/tree/rooted-tree.qza" metadata_microecoTRIPLICASino<- "/home/victor/Escritorio/Microeco/metadatasnuevos/metadata_microecoTRIPLICASino.csv"

Constructing microtable object

MicroEcoDataObjectTripIno <- qiime2meco(table_microecoTriplicates, sample_table = metadata_microecoTRIPLICASino, taxonomy_table = taxonomy_microecoTriplicates, phylo_tree = tree_microecoTriplicates, rep_fasta = rep_microecoTriplicates, auto_tidy = TRUE)

Differential abundance analysis

diffMicroecoTripIno<-trans_diff$new( dataset = MicroEcoDataObjectTripIno, method = c("rf")[1], group = "Type", taxa_level = "all", filter_thres = 0, alpha = 0.05, p_adjust_method = "fdr", transformation = NULL, remove_unknown = TRUE, lefse_subgroup = NULL, lefse_min_subsam = 10, lefse_norm = 1e+06, nresam = 0.6667, boots = 30, rf_ntree = 1000, group_choose_paired = NULL, metagenomeSeq_count = 1, ALDEx2_sig = c("wi.eBH", "kw.eBH"), by_group = NULL, by_ID = NULL, beta_pseudo = .Machine$double.eps, )

Plotting DA result as cladogram

diffMicroecoTripIno$plot_diff_cladogram( color = RColorBrewer::brewer.pal(8, "Dark2"), group_order = c("LDPE","LLDPE","FILM","No plastic"), use_taxa_num = 200, filter_taxa = NULL, use_feature_num = 100, clade_label_level = 4, select_show_labels = NULL, only_select_show = FALSE, sep = "|", branch_size = 0.2, alpha = 0.2, clade_label_size = 2, clade_label_size_add = 5, clade_label_size_log = exp(1), node_size_scale = 1, node_size_offset = 1, annotation_shape = 22, annotation_shape_size = 5)

ChiLiubio commented 4 months ago

Hi. I run the steps and get this. test

I am using microeco v1.8.0, same with current CRAN v1.7.1. The session info is:

sessionInfo() R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] ggplot2_3.5.0 Biostrings_2.70.3 GenomeInfoDb_1.38.8 XVector_0.42.0
[5] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 microeco_1.8.0

loaded via a namespace (and not attached): [1] gtable_0.3.4 lattice_0.22-5 vctrs_0.6.5
[4] tools_4.3.3 bitops_1.0-7 generics_0.1.3
[7] yulab.utils_0.1.4 parallel_4.3.3 tibble_3.2.1
[10] fansi_1.0.6 cluster_2.1.6 pkgconfig_2.0.3
[13] Matrix_1.6-5 ggplotify_0.1.2 data.table_1.15.2
[16] RColorBrewer_1.1-3 lifecycle_1.0.4 GenomeInfoDbData_1.2.11 [19] compiler_4.3.3 farver_2.1.1 stringr_1.5.1
[22] textshaping_0.3.7 treeio_1.26.0 munsell_0.5.0
[25] permute_0.9-7 ggtree_3.10.1 ggfun_0.1.4
[28] RCurl_1.98-1.14 lazyeval_0.2.2 pillar_1.9.0
[31] crayon_1.5.2 tidyr_1.3.1 MASS_7.3-60.0.1
[34] cachem_1.0.8 vegan_2.6-4 nlme_3.1-164
[37] aplot_0.2.2 tidyselect_1.2.1 digest_0.6.35
[40] stringi_1.8.3 dplyr_1.1.4 reshape2_1.4.4
[43] purrr_1.0.2 labeling_0.4.3 splines_4.3.3
[46] fastmap_1.1.1 grid_4.3.3 colorspace_2.1-0
[49] cli_3.6.2 magrittr_2.0.3 patchwork_1.2.0
[52] randomForest_4.7-1.1 utf8_1.2.4 ape_5.7-1
[55] withr_3.0.0 scales_1.3.0 igraph_2.0.3
[58] ragg_1.3.0 memoise_2.0.1 mgcv_1.9-1
[61] gridGraphics_0.5-1 rlang_1.1.3 Rcpp_1.0.12
[64] glue_1.7.0 tidytree_0.4.6 jsonlite_1.8.8
[67] rstudioapi_0.16.0 R6_2.5.1 plyr_1.8.9
[70] systemfonts_1.0.6 fs_1.6.3 zlibbioc_1.48.2

BiggusDickus666 commented 4 months ago

Hi @ChiLiubio I contrasted my info session with yours along with the info session of a lab partner of mine, and I noticed it was all about the R version. Mine was R4.2. We run the same code utilizing the same .qza in a newer R version, and labels appeared on the cladogram without a problem. Something as simple as that. Thank you very much for your time and effort, and sorry for any inconvenience!!

ChiLiubio commented 4 months ago

Ok. Glad to see it is solved!