get_upset {MicrobiotaProcess} | R Documentation

## generate the dataset for upset of UpSetR

### Description

generate the dataset for upset of UpSetR

### Usage

    get_upset(obj, ...)

    ## S4 method for signature 'data.frame'
    get_upset(obj, sampleda, factorNames, threshold = 0)

    ## S4 method for signature 'phyloseq'
    get_upset(obj, ...)

### Arguments

`obj` | object, phyloseq or data.frame, if it is data.frame, the shape of it should be row sample * columns features.
`...,` | additional parameters.
`sampleda` | data.frame, if the obj is data.frame, the sampleda should be provided.
`factorNames` | character, the column names of factor in sampleda
`threshold` | integer, default is 0.

### Value

a data.frame for the input of 'upset' of 'UpSetR'.

### Author(s)

Shuangbin Xu

### Examples

    data(test_otu_data)
    upsetda <- get_upset(test_otu_data, factorNames="group")
    otudafile <- system.file("extdata", "otu_tax_table.txt",
                             package="MicrobiotaProcess")
    samplefile <- system.file("extdata","sample_info.txt",
                             package="MicrobiotaProcess")
    otuda <- read.table(otudafile, sep="\t", header=TRUE,
                        row.names=1, check.names=FALSE,
                        skip=1, comment.char="")
    sampleda <- read.table(samplefile,sep="\t",
                           header=TRUE, row.names=1)
    head(sampleda)
    otuda <- otuda[sapply(otuda, is.numeric)]
    otuda <- data.frame(t(otuda), check.names=FALSE)
    head(otuda[1:5, 1:5])
    upsetda2 <- get_upset(obj=otuda, sampleda=sampleda,
                         factorNames="group")
    #Then you can use `upset` of `UpSetR` to visualize the results.
    #library(UpSetR)
    #upset(upsetda, sets=c("B","D","M","N"), sets.bar.color = "#56B4E9",
    #      order.by = "freq", empty.intersections = "on")

[Package MicrobiotaProcess version 1.2.2 Index]