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b/man/Cohesion.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/7.stability.R |
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\name{Cohesion} |
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\alias{Cohesion} |
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\alias{plot.cohesion} |
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\title{Cohesion calculation} |
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\usage{ |
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Cohesion(otutab, reps = 200, threads = 1, mycor = NULL, verbose = TRUE) |
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\method{plot}{cohesion}(x, group, metadata, mode = 1, ...) |
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} |
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\arguments{ |
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\item{otutab}{otutab} |
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\item{reps}{iteration time} |
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\item{threads}{threads} |
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\item{mycor}{a correlation matrix you want to use, skip the null model build when mycor is not NULL, default: NULL} |
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\item{verbose}{verbose} |
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\item{x}{\code{Cohesion()} result (cohesion object)} |
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\item{group}{group name in colnames(metadata)} |
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\item{metadata}{metadata} |
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\item{mode}{plot mode, 1~2} |
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\item{...}{additional arguments for \code{\link[pcutils]{group_box}} (mode=1) or \code{\link[pcutils]{group_box}} (mode=2)} |
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} |
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\value{ |
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Cohesion object: a list with two dataframe |
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a ggplot |
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} |
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\description{ |
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Cohesion calculation |
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Plot cohesion |
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} |
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\examples{ |
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\donttest{ |
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data("otutab", package = "pcutils") |
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# set reps at least 99 when you run. |
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Cohesion(otutab[1:50, ], reps = 19) -> cohesion_res |
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if (requireNamespace("ggpubr")) { |
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plot(cohesion_res, group = "Group", metadata = metadata, mode = 1) |
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plot(cohesion_res, group = "Group", metadata = metadata, mode = 2) |
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} |
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} |
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} |
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\references{ |
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Herren, C. M. & McMahon, K. (2017) Cohesion: a method for quantifying the connectivity of microbial communities. doi:10.1038/ismej.2017.91. |
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} |