diff --git a/paper/table1_publication.svg b/paper/table1_publication.svg new file mode 100644 index 00000000..6da525dc --- /dev/null +++ b/paper/table1_publication.svg @@ -0,0 +1,1570 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MiscMetabar + + + Other packages + + + 1. Mia — 2. microViz — 3.MicrobiotaProcess — 4. Phylosmith + + + Conversion to physeq + + + Conversion from physeq + + + Describe + + + summary_plot_pq() + + + krona() + + + sankey_pq() + + + accu_plot() + + + SRS_curve_pq() + + + clean_pq() + + + filter_asv_blast() + + + asv2otu() + + + lulu_pq() + + + E + x + p + l + o + r + e + + + Alpha-diversity + + + hill_pq() + + + Beta-diversity + + + ggvenn_pq() + + + upset_pq() + + + graph_test_pq() + + + adonis_pq() + + + plot_tsne_pq() + + + plot_tax_pq() + + + circle_pq() + + + amplicon::tax_circlize() + + + Compare 2 modalities + + + biplot_pq() + + + compare_pairs_pq() + + + Differential abundance + + + plot_deseq2_pq() + + + Taxonomy + + + blast_pq() + + + heat_tree_pq() + + + tax_datatable() + + + multitax_bar_pq() + + + treemap_pq() + + + Reproduce + + + write_pq() + + + read_pq() + + + list_fastq_files() + + + track_wkflow() + + + track_wkflow_samples() + + + MakeTreeSEFromPhyloseq() + + + 1 + + + as.MPSE() + + + 3 + + + MakePhyloseqFromTreeSE() + + + 1 + + + as.phyloseq() + + + 3 + + + mp_plot_rarecurve() + + + 3 + + + Transform + + + See also table 2 + + + EstimateDiversity() + + + 1 + + + mp_plot_alpha() + + + 3 + + + Alpha_diversity_graph() + + + 4 + + + mp_plot_venn() + + + 3 + + + dist_permanova() + + + 2 + + + Mp_adonis() + + + 3 + + + tsne_phyloseq() + + + 4 + + + PlotAbundance() + + + 1 + + + comp_barplot() + + + 2 + + + mp_plot_abundance() + + + 3 + + + Phylogeny_profile() + + + 4 + + + + Mp_diff_analysis() + + + 3 + + A + C + B + D + E + F + G + H + I + + + Fig.2 + + + + + + + + + + diff --git a/paper/tengeler_MiscMetabar.svg b/paper/tengeler_MiscMetabar.svg new file mode 100644 index 00000000..dbc07d33 --- /dev/null +++ b/paper/tengeler_MiscMetabar.svg @@ -0,0 +1,12387 @@ + +151 taxa 485 932 sequences 1 534 occurences6 taxonomic levels4 variables 27 samplesSequences length: No refseq slot@otu_table@tax_table@sam_data@refseqTaxa(OTUs, ASVs, ...)SamplesMin nb seq per sample (A291772Nb samples with less than 500 seq : 0Min nb seq per taxa: 173 (1 ASV)Min seq length: No refseq slotMax nb seq 1 taxa in 1 sample: 17722Max nb of sample for one taxa (1726472): 27Nb of taxa present in 1 sample only: 0ADHDControl304050607080Richness (Hill 0)patient_status1020Shannon (Hill 1)4812Simpson (Hill 2)Hill Number 0 Control-ADHDHill Number 1 Control-ADHDHill Number 2 Control-ADHD-10-50510Differences in mean levels (value and confidence intervals at 95%)Tuckey HSD testing for differences in mean Hill numbers531141745312631121341434212111102040Intersection size050100Set sizeControl_Cohort_1ADHD_Cohort_3Control_Cohort_3ADHD_Cohort_2Control_Cohort_2ADHD_Cohort_1patient_status_vs_cohortBacteriaFirmicutesVerrucomicrobiaBacteroidetesProteobacteriaCyanobacteriaClostridiaErysipelotrichiaVerrucomicrobiaeBacteroidiaGammaproteobacteriaMelainabacteriaClostridialesErysipelotrichalesVerrucomicrobialesBacteroidalesOceanospirillalesEnterobacterialesGastranaerophilalesRuminococcaceaeErysipelotrichaceaeLachnospiraceaeVerrucomicrobiaceaeClostridiaceae_1PorphyromonadaceaeBacteroidales_S24-7_groupBacteroidaceaePrevotellaceaeRikenellaceaeHalomonadaceaeEnterobacteriaceaeChristensenellaceaeEubacteriaceae[Eubacterium]_coprostanoligenes_group[Clostridium]_innocuum_groupDielmaEpulopisciumHoldemaniaAkkermansiaErysipelatoclostridiumClostridium_sensu_stricto_1Parabacteroidesuncultured_bacteriumunculturedCoprobacterBacteroidesParaprevotellaBarnesiellaOdoribacterAlistipesHalomonasEscherichia-ShigellaCoprococcus_2FusicatenibacterLachnoclostridium[Ruminococcus]_gnavus_groupHungatellaunculturedEisenbergiella[Eubacterium]_rectale_group[Ruminococcus]_gauvreauii_groupRoseburiaAnaerostipes[Eubacterium]_xylanophilum_group[Eubacterium]_fissicatena_groupCatabacterLachnospiraceae_ND3007_groupRuminococcaceae_UCG-014ButyricicoccusRuminococcaceae_UCG-004unculturedFlavonifractorRuminiclostridium_9AnaerotruncusRuminococcus_2FaecalibacteriumRuminococcus_1SubdoligranulumRuminiclostridium_5Ruminococcaceae_UCG-013EubacteriumBlautia 1.0 14.0 30.4 51.1 77.1110.0151.0 182 16200 58300126000220000340000486000..2..1NodesCohort_1 (10 sam.)Cohort_2 (10 sam.)Cohort_3 (7 sam.)0(0%)0(0%)0(0%)24(16%)2(1%)8(5%)117(77%)-20-100102030BacteroidesFaecalibacteriumParaprevotellaHungatellaRuminococcaceae_UCG-013Ruminococcaceae_UCG-014ParabacteroidesunculturedCatabacter[Ruminococcus]_gauvreauii_groupBlautiataxlog2FoldChangecol_taxBacteroidetesFirmicutesChange in abundance for patient_status (top:ADHD vs down:Control)ADHDControlBacteroidetesCyanobacteriaFirmicutesProteobacteriaVerrucomicrobiaBacteroidiaMelainabacteriaClostridiaErysipelotrichiaGammaproteobacteriaVerrucomicrobiae012345012345BacteroidalesGastranaerophilalesClostridialesErysipelotrichalesEnterobacterialesOceanospirillalesVerrucomicrobialesAbundanceLVL3Control (14 samples)Control (14 samples)ADHD (13 samples)ADHD (13 samples)6625255741276002356822263199871707614726129481034681787192560250404534447142964229387938753743364433623226318731443116304530402693265524872466239223072230195218631732169616631626130711701079107910689388607466465334341726471517264791726472131726471321726471817264740172647221726476117264714517264781726471901726471917264734172647166172647167172647531726471891726472917264748172647271726472517264747172647241726472172647261726473117264711726470Samples-5.0-2.50.02.55.0Abstats::reorder(OTU, Abundance)modalityADHDControl0255075010000200003000040000Number of sequencesNumber of OTUs (with standard error)factA110A111A12A13A14A15A16A17A18A19A21A210A22A23A24A25A26A27A28A29A33A34A35A36A37A38A39ABCDEFGHI