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#' @title method extensions to show for diffAnalysisClass objects.
#' @rdname show-methods
#' @param object object, `diffAnalysisClass` class
#' @importFrom methods show
#' @author Shuangbin Xu
#' @return print info
#' @export
#' @examples
#' # don't run in examples
#' #data(kostic2012crc)
#' #kostic2012crc
#' #head(phyloseq::sample_data(kostic2012crc),3)
#' #kostic2012crc <- phyloseq::rarefy_even_depth(kostic2012crc,rngseed=1024)
#' #table(phyloseq::sample_data(kostic2012crc)$DIAGNOSIS)
#' #set.seed(1024)
#' #diffres <- diff_analysis(kostic2012crc, classgroup="DIAGNOSIS",
#' # mlfun="lda", filtermod="fdr",
#' # firstcomfun = "kruskal.test",
#' # firstalpha=0.05, strictmod=TRUE,
#' # secondcomfun = "wilcox.test",
#' # subclmin=3, subclwilc=TRUE,
#' # secondalpha=0.01, lda=3)
#' #show(diffres)
setMethod("show",
"diffAnalysisClass",
function(object){
originalD <- object@originalD
cat(paste0("The original data: ", ncol(originalD),
" features and ", nrow(originalD)," samples"),
fill=TRUE)
sampleda <- object@sampleda
cat(paste0("The sample data: ", ncol(sampleda), " variables and ", nrow(sampleda), " samples"),
fill=TRUE)
taxda <- object@taxda
if(!is.null(taxda)){cat(paste0("The taxda contained ", nrow(taxda), " by ",ncol(taxda), " rank"),
fill=TRUE)}
else{cat("The taxda is NULL",fill=TRUE)}
kwres <- object@kwres
numfirstf <- nrow(kwres[kwres$pvalue<=0.05 & !is.na(kwres$pvalue),])
firstfun <- extract_args(object, "firstcomfun")
filtermod <- extract_args(object, "filtermod")
alphafold <- extract_args(object, "firstalpha")
cat(paste0("after first test (",firstfun,") number of feature (", filtermod,"<=",alphafold,"):",
numfirstf),fill=TRUE)
secondvars <- get_second_true_var(object)
secondfun <- extract_args(object, "secondcomfun")
cat(paste0("after second test (",secondfun,") number of significantly discriminative feature:",
nrow(secondvars)),
fill=TRUE)
mlres <- as.data.frame(object)
uncertain <- length(grep("__un_", mlres$f))
mlmethod <- extract_args(object, "mlfun")
cat(paste0("after ",mlmethod,", Number of discriminative features: ",
nrow(mlres), " (certain taxonomy classification:",
nrow(mlres) -uncertain ,
"; uncertain taxonomy classication: ",uncertain,")"),
fill=TRUE)
}
)
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