get_upset: generate the dataset for upset of UpSetR

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

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

## Not run: 
data(test_otu_data)
test_otu_data %<>% as.phyloseq()
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")

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.