get_upset {MicrobiotaProcess} | R Documentation |
generate the dataset for upset of UpSetR
get_upset(obj, ...) ## S4 method for signature 'data.frame' get_upset(obj, sampleda, factorNames, threshold = 0) ## S4 method for signature 'phyloseq' get_upset(obj, ...)
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. |
a data.frame for the input of 'upset' of 'UpSetR'.
Shuangbin Xu
## 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)