microbiota/amplicon: Statistics and visualization for microbiome data

A basic statistics and plotting pipeline for amplicon data. 1. Alpha boxplot with ANOVA + Tukey test / LSD.test; 2. Alpha rarefraction curve in samples and groups with standard error; 3. PCoA plot with confidence ellipse and Adonis P-value; 4. Constrained PCoA with variant, P-value and confidence ellipse; 5. Taxonomy stackplot in group and sample. 1.0.1 add beta_cpcoa_dis.R support constrained distance matrix 1.1.0 add more than 10 functions 1.1.1 2020-06-15 Update citation and beta_pcao example 1.1.2 2020-06-20 Add alpha_sample_rare plot sample rarefaction boxplot 1.1.3 2020-08-03 Debug code in R 4.0.2, such tax_stackplot 1.1.4 2020-09-03 Update tax_wordcloud, add tax_stack_clust for tree+stackplot 1.1.5 2020-09-05 Fix bug "下标出界" in beta_pcoa_stat.R, add intersect metadata and distance matrix 1.11.0 2021-04-03 Fix bug metadata only 2 columns cause "Error in metadata[, groupID] : 量度数目不对" 1.11.1 2021-04-04 Using multcomp 解决字母顺序相反的问题(alpha_boxplot);tax_stackplot中修改Unassigned至Other组;compare增加不标准化的normlize参数 1.14.1 2021-10-16 陈同新增堆叠柱状图分面功能 1.14.2 2021-12-12 文涛更新tax_treemap.R 1.14.2 2022-11-06 文涛更新alpha_boxplot.R，default keep outlier 1.18.0 2023-1-27 update all R package 1.18.1 2023-1-28 adonis to adonis2 in beta_pcoa_stat.R 1.19.0 2023-4-25 adonis2 data strcutre change: adonis_table$aov.tab$`Pr(>F)`[1] to adonis_table$`Pr(>F)`[1] in beta_pcoa_stat.R

install.packages("remotes")
remotes::install_github("microbiota/amplicon")