get_upset: generate the dataset for upset of UpSetR

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

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")

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.