Package: ggpicrust2 1.7.4

ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.

Authors:Chen Yang [aut, cre], Liangliang Zhang [aut]

ggpicrust2_1.7.4.tar.gz

ggpicrust2_1.7.4.tar.gz(r-4.4-noble)
ggpicrust2_1.7.4.tgz(r-4.4-emscripten)ggpicrust2_1.7.4.tgz(r-4.3-emscripten)
ggpicrust2.pdf |ggpicrust2.html✨
ggpicrust2/json (API)
NEWS

# Install 'ggpicrust2' in R:

install.packages('ggpicrust2', repos = c('https://cafferychen777.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cafferychen777/ggpicrust2/issues

Datasets:

daa_annotated_results_df - Differentially Abundant Analysis Results with Annotation
daa_results_df - DAA Results Dataset
kegg_abundance - KEGG Abundance Dataset
ko_abundance - KO Abundance Dataset
metacyc_abundance - MetaCyc Abundance Dataset
metadata - Metadata for ggpicrust2 Demonstration

On CRAN:

16s-rrna functional-data metagenomic-analysis metagenomics microbiome microbiota picrust2 tax4fun2 visualization

7.51 score 109 stars 84 scripts 773 downloads 10 exports 226 dependencies

Last updated 10 days agofrom:d0815f6ea4. Checks:OK: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 13 2024

Exports:compare_daa_results compare_metagenome_results ggpicrust2 import_MicrobiomeAnalyst_daa_results ko2kegg_abundance pathway_annotation pathway_daa pathway_errorbar pathway_heatmap pathway_pca

Dependencies:abind ALDEx2 ape aplot askpass backports BH biglm Biobase BiocGenerics BiocParallel bit bit64 bitops boot brio broom callr car carData caTools chemometrics circlize class cli clipr clue cluster coda codetools coin colorspace cowplot cplm cpp11 crayon curl data.table DBI DelayedArray deldir DEoptimR Deriv desc DESeq2 diffobj digest directlabels doBy dplyr e1071 edgeR evaluate fansi farver fBasics forcats foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges getopt GGally ggfun ggh4x ggplot2 ggplotify ggprism ggrepel ggstats ggtree glmmTMB glmnet GlobalOptions glue gplots gridGraphics gss gtable gtools hash hms httr interp IRanges isoband iterators jpeg jsonlite KernSmooth labeling lambda.r lars lattice latticeExtra lazyeval lefser libcoin lifecycle limma lme4 lmerTest locfit logging Maaslin2 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust metagenomeSeq mgcv microbenchmark MicrobiomeStat mime minqa modeest modelr modeltools multcomp multtest munsell mvtnorm NADA nlme nloptr nnet numDeriv openssl optparse patchwork pbapply pbkrtest pcaPP permute pheatmap pillar pkgbuild pkgconfig pkgload pls plyr png praise prettyunits processx progress proxy ps pscl purrr quadprog quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppGSL RcppParallel RcppZiggurat Rdpack readr reformulas reshape2 Rfast rlang rmutil robustbase rpart rprojroot S4Arrays S4Vectors sandwich scales shape snow som SparseArray SparseM spatial stable stabledist statip statmod stringi stringr SummarizedExperiment survival sys testthat TH.data tibble tidyr tidyselect tidytree timeDate timeSeries TMB treeio truncnorm tweedie tzdb UCSC.utils utf8 vctrs vegan viridisLite vroom waldo withr Wrench XVector yulab.utils zCompositions zlibbioc zoo

ggpicrust2 vigenett

Caffery Yang

Rendered fromusing_ggpicrust2.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-13
Started: 2023-05-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compare the Consistency of Statistically Significant Features	compare_daa_results
Compare Metagenome Results	compare_metagenome_results
Differentially Abundant Analysis Results with Annotation	daa_annotated_results_df
DAA Results Dataset	daa_results_df
This function integrates pathway name/description annotations, ten of the most advanced differential abundance (DA) methods, and visualization of DA results.	ggpicrust2
Import Differential Abundance Analysis (DAA) results from MicrobiomeAnalyst	import_MicrobiomeAnalyst_daa_results
KEGG Abundance Dataset	kegg_abundance
KO Abundance Dataset	ko_abundance
Convert KO abundance in picrust2 export files to KEGG pathway abundance	ko2kegg_abundance
MetaCyc Abundance Dataset	metacyc_abundance
Metadata for ggpicrust2 Demonstration	metadata
Pathway information annotation of "EC", "KO", "MetaCyc" pathway	pathway_annotation
Predictional functional patwhay differential abundance (DA)	pathway_daa
The function pathway_errorbar() is used to visualize the results of functional pathway differential abundance analysis as error bar plots.	pathway_errorbar
Create pathway heatmap	pathway_heatmap
Perform Principal Component Analysis (PCA) on functional pathway abundance data	pathway_pca