R/method-show.R

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

#' @title method extensions to show for diffAnalysisClass or alphasample objects.
#' @rdname show-methods
#' @param object object, diffAnalysisClass or alphasample class
#' @importFrom methods show
#' @author Shuangbin Xu
#' @return print info
#' @export
#' @examples
#' \dontrun{
#' data(kostic2012crc)
#' kostic2012crc %<>% as.phyloseq()
#' 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)}

      
      firstvars <- extract_first_vars(obj=object) 
      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,"):", 
      length(firstvars)),fill=TRUE)
      secondvars <- get_second_true_var(object)
      #secondfun <- extract_args(object, "secondcomfun")
      secondfun <- check_second_fun(obj=object)
      cat(paste0("after second test (",secondfun,") number of significantly discriminative feature:", 
      		   nrow(secondvars)),
          fill=TRUE)
      mlres <- object@result 
      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)
    }
)


extract_first_vars <- function(obj){
    filtermod <- extract_args(obj, "filtermod")
    firstalpha <- extract_args(obj, "firstalpha")
    kwres <- obj@kwres
    if (filtermod !="pvalue"){
        varsfirst <- kwres[kwres$fdr<=firstalpha& !is.na(kwres$fdr),,drop=FALSE]
    }else{
        varsfirst <- kwres[kwres$pvalue<=firstalpha&!is.na(kwres$pvalue),,drop=FALSE]
    }
    return (as.vector(varsfirst$f))
}

check_second_fun <- function(obj){
    subclass <- extract_args(obj, "subclass")
    classgroup <- extract_args(obj, "classgroup")
    strictmod <- extract_args(obj, "strictmod")
    clmin <- extract_args(obj, "clmin")
    clwilc <- extract_args(obj, "clwilc")
    fcfun <- extract_args(obj, "fcfun")
    secondcomfun <- extract_args(obj, "secondcomfun")
    subclmin <- extract_args(obj, "subclmin")
    subclwilc <- extract_args(obj, "subclwilc")
    if (!is.null(subclass) && strictmod){
        submin <- min(table(obj@sampleda[[subclass]]))
        if (submin >= subclmin && subclwilc){
            secondfun <- paste(secondcomfun, "and", fcfun)
        }else{
            secondfun <- fcfun
        }
    }else{
        groupmin <- min(table(obj@sampleda[[classgroup]]))
        if (groupmin >= clmin && clwilc){
            secondfun <- paste(secondcomfun, "and", fcfun)
        }else{
            secondfun <- fcfun
        }
    }
    return (secondfun)
}

#' @rdname show-methods
#' @exportMethod show
setMethod("show", "alphasample", function(object){
    print.alphasample(object)
})

print.alphasample <- function(object){
    msg <- "'alphasample' S4 object"
    sampleda <- object@sampleda
    if (!is.null(sampleda)){
        smsg <- sampleda
    }else{
        smsg <- "The 'alphasample' does not have sampleda slot."
    }
    cat (msg, fill=TRUE)
    cat ("The alpha diversity index :", fill=TRUE)
    print (head(object@alpha))
    if (is.character(smsg)){
        cat (smsg, fill=TRUE)
    }else{
        cat ("The sample information is present in 'alphasample':", fill=TRUE)
        print (head(sampleda))
    }
}

#' @rdname show-methods
#' @exportMethod show
setMethod("show", "MPSE", function(object){
    object %>% print()
})


#' @title print some objects
#' @name print
#' @param x Object to format or print.
#' @param ... Other arguments passed on to individual methods.
#' @param n Number of rows to show. If `NULL`, the default, will print all rows
#'   if less than option `tibble.print_max`. Otherwise, will print
#'   `tibble.print_min` rows.
#' @param width Width of text output to generate. This defaults to `NULL`, which
#'   means use `getOption("tibble.width")` or (if also `NULL`)
#'   `getOption("width")`; the latter displays only the columns that fit on one
#'   screen. You can also set `options(tibble.width = Inf)` to override this
#'   default and always print all columns.
#' @param max_extra_cols Number of extra columns to print abbreviated information for,
#'   if the width is too small for the entire tibble. If `NULL`, the default,
#'   will print information about at most `tibble.max_extra_cols` extra columns.
#' @param max_footer_lines integer maximum number of lines for the footer.
#' @return print information
NULL

#' @rdname print
#' @method print MPSE
#' @export
print.MPSE <- function(x, ..., n = NULL, width = NULL, max_extra_cols = NULL, max_footer_lines = NULL){
    show.mpse <- getOption(x = "MPSE_show_tbl", default = TRUE)
    if (show.mpse){
        print2.MPSE(x, ..., n = n, width = width, max_extra_cols = max_extra_cols)
    }else{
        print1.MPSE(x, ...)
    }
}

print1.MPSE <- function(x, ...){
    writeLines(formatted_out("The otutree (treedata object) of the MPSE object is: "))
    if (!is.null(x@otutree)){
        show(x@otutree)
    }else{
        writeLines("NULL")
    }
    writeLines(formatted_out("The taxatree (treedata object) of the MPSE object is: "))
    if (!is.null(x@taxatree)){
        show(x@taxatree)
    }else{
        writeLines(formatted_out("NULL"))
    }
    writeLines(formatted_out("The reference sequence (XStringSet object) of the MPSE object is: "))
    if (!is.null(x@refseq)){
        show(x@refseq)
    }else{
        writeLines("NULL")
    }
    writeLines(formatted_out("The abundance and sample data of the MPSE object are: "))
    f <- methods::getMethod(f="show", signature = "SummarizedExperiment")
    f(x)
}

print2.MPSE <- function(x, ..., n = NULL, width = NULL, max_extra_cols = NULL, max_footer_lines=NULL) {
    total_nrows <- nrow(x) * ncol(x)
    if (is.null(n)){
        n <- 10
    }

    if (total_nrows <= n){
        n <- total_nrows
    }
    if (!is.null(x@taxatree)){
        taxonomy <- x@taxatree %>% 
                    #select("nodeClass") %>%
                    dplyr::filter(! .data$nodeClass %in% c("Root") & !.data$isTip, keep.td=FALSE) %>%
                    pull(.data$nodeClass) %>%
                    unique() %>%
                    paste(collapse=", ")
    }else{
        taxonomy <- NULL
    }

    if (n < nrow(x)){
        tmpx <- x[seq_len(n), seq_len(min(1, ncol(x))), drop=FALSE]
    }else{
        tmpx <- x[, seq_len(min(round(n/nrow(x))+1, ncol(x))), drop=FALSE]
    }
    tmpx %<>% 
        as_tibble() %>% 
        drop_class(class=c("tbl_mpse", "grouped_df_mpse")) #%>%
        #add_class(new="TBL_MPSE")
    
    formatted_mpse_setup <- tbl_format_setup(x = tmpx, width = width, ..., n = n, 
                                             max_extra_cols = max_extra_cols, 
                                             max_footer_lines = max_footer_lines
                            )

    formatted_mpse_setup <- modify_tbl_format_setup(formatted_mpse_setup, totalX = total_nrows)
    
    format_comment <- getFromNamespace("format_comment", "pillar")

    subtitle <- sprintf(" OTU=%s | Samples=%s | Assays=%s | Taxonomy=%s",
                      nrow(x),
                      ncol(x),
                      SummarizedExperiment::assayNames(x) %>% paste(collapse=", "),
                      ifelse(is.null(taxonomy), "NULL", taxonomy)
                ) %>% 
                format_comment(width=nchar(.) + 5) %>% 
                pillar::style_subtle()

    header <- pillar::tbl_format_header(tmpx, formatted_mpse_setup) %>%
              append(subtitle, after=1)
    body <- pillar::tbl_format_body(tmpx, formatted_mpse_setup)
    footer <- pillar::tbl_format_footer(tmpx, formatted_mpse_setup)
    footer <- modify_tbl_format_footer(footer)
    writeLines(c(header, body, footer))
    invisible(x)
}

#' @importFrom pillar tbl_format_setup
modify_tbl_format_setup <- function(x, totalX, ...){ 
    tmpxx <- x$tbl_sum %>%
             strsplit(" ") %>%
             unlist()
    tmpxx <- paste(getFromNamespace("big_mark", "pillar")(totalX), tmpxx[2], tmpxx[3])
    names(tmpxx) <- c("A MPSE-tibble (MPSE object) abstraction")
    x$tbl_sum <- tmpxx
    x$rows_total <- totalX
    x$rows_missing <- totalX - nrow(x$df)
    return(x)
}

modify_tbl_format_footer <- function(x, ...){
    index.1 <- grepl('colnames\\(\\)', x)
    index.2 <- which(grepl('print\\(', x))
    if (any(index.1)){
        x <- x[!index.1]
    }
    if (length(index.2) > 0 && index.2 > length(x)){
        advice <- paste0("# ", cli::symbol$info, " Use `print(n = ...)` to see more rows.")
        x <- c(x, pillar::style_subtle(advice))
    }
    return(x)
}

#' @method print tbl_mpse
#' @rdname print
#' @export
print.tbl_mpse <- function(x, ..., n = NULL, width = NULL, max_extra_cols = NULL){
    formatted_tb <- x %>% format(..., n = n, width = width, max_extra_cols = max_extra_cols)
    if (valid_names(x, type="tbl_mpse")){
        new_head = "A tbl_mpse (which can be converted to MPSE via as.MPSE) abstraction:"
        formatted_tb_mpse <-
            formatted_tb %>% 
            {
               x = (.);
               x[1] = gsub("(A tibble:)", new_head, x[1]);
               x
            }
        writeLines(formatted_tb_mpse)
    }else{
        writeLines(formatted_tb)
    }
    invisible(x)
}

#' @method print grouped_df_mpse
#' @rdname print
#' @export
print.grouped_df_mpse <- function(x, ..., n = NULL, width = NULL, max_extra_cols = NULL){
    formatted_tb <- x %>% format(..., n = n, width = width, max_extra_cols = max_extra_cols)
    if (valid_names(x, type="grouped_df_mpse")){
        new_head = "A grouped_df_mpse (which can be converted to MPSE via as.MPSE) abstraction:"
        formatted_grouped <- 
            formatted_tb %>%
            {
                x = (.);
                x[1] = gsub("(A tibble:)", new_head, x[1]);
                x
            }
        writeLines(formatted_grouped)
    }else{
        writeLines(formatted_tb)
    }
    invisible(x)
}

#' @method print rarecurve
#' @rdname print
#' @export
print.rarecurve <- function(x, ..., n = NULL, width = NULL, max_extra_cols = NULL){
    formatted_tb <- x$data %>% format(..., n =  n, width = width, max_extra_cols = max_extra_cols)
    new_head = "A rarecurve (which can be visualized via ggrarecurve) abstraction:"

    format_rare <- 
        formatted_tb %>%
        {
            x = (.);
            x[1] = gsub("(A tibble:)", new_head, x[1]);
            x
        }
    writeLines(format_rare)

    invisible(x)
}