dynPlots: dynPlot Diagnostic plots

In etheleon/metamaps: MetamapsDB: R package for querying Metagenomics data against Metabolic Pathways and Gene Centric Assemblies

Description

dynPlot Diagnostic plots

Usage

dynPlots(dynList, indivPlots = T)

Arguments

dyn	output from dynamicThreshold

Examples

## Not run: 
    connect("yourDomain", password="yourPassword")
    newblerDir= "~/simulation_fr_the_beginning/reAssemble/everybodyelse/data/newbler/"
    dynList = scg  %>% gsub("ko:", "", .) %>% mclapply(dynamicThreshold, root=newblerDir, mc.cores=20)
    dynList = scg  %>% gsub("ko:", "", .) %>% head(n=1) %>% lapply(dynamicThreshold, root=newblerDir)
    pdf("thresholdPlots.pdf", width=10)
    plotDF = dynPlots(dynList, F)
    dev.off()
    pdf("abundance.pdf", width=10)
    lapply(plotDF$details,"[[", 1)
    dev.off()
    plotDF$p %>% ggsave(file="summaryPlot.pdf", w=10)
    plotDF$violin %>% ggsave(file="violin.pdf", w=10, h=4)

## End(Not run)

etheleon/metamaps documentation built on May 16, 2019, 9:05 a.m.