R/2_sumexp_to_dt.R

In bhagwataditya/importomics: Unified statistal Modeling of Omics Data

#' @rdname sumexp_to_longdt
#' @export
sumexp_to_widedt <- function(
    object,
    fvars = autonomics::fvars(object),
    assay = assayNames(object)[1]
){

    # Assert
    assert_is_all_of(object, 'SummarizedExperiment')
    assert_is_subset(fvars, fvars(object))

    # Extract
    wide1 <- fdt(object)[, unique(c('feature_id', fvars)), with = FALSE]
    if (is.numeric(assay))  assay <- assayNames(object)[assay]
    for (ass in assay){
        exprs1 <- data.table(assays(object)[[ass]])
        if (length(assay) > 1)  colnames(exprs1) %<>% paste0(ass, '.', .)
        wide1  %<>% cbind(exprs1)
    }
    wide1[, feature_id := factor(feature_id, unique(fdt(object)$feature_id))]

    # Return
    wide1[]
}



#' SummarizedExperiment to data.table
#'
#' @details
#' \itemize{
#'    \item \code{sumexp_to_widedt}:    feature          x sample
#'    \item \code{sumexp_to_subrep_dt}: feature.subgroup x replicate
#'    \item \code{sumexp_to_longdt}:    feature.sample
#' }
#' @param object sumexp
#' @param subgroup subgroup (sym)
#' @param fvars  additional fvars to include in table
#' @param svars  additional svars to include in table
#' @param assay  matrix in assays(object) to be used
#' @return data.table
#' @examples
#' # Atkin Hypoglycemia
#'    file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
#'    object <- read_metabolon(file)
#'    sumexp_to_widedt(object)
#'    sumexp_to_longdt(object)
#'    sumexp_to_subrep_dt(object)
#'
#' # Fukuda
#'    file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
#'    object <- read_maxquant_proteingroups(file)
#'    values(object)
#'    fdt(object)
#'    object %<>% impute()
#'    table(fdt(object)$imputed)
#'    sumexp_to_longdt(object)
#'    sumexp_to_widedt(object)
#'    sumexp_to_longdt(object)
#' @export
sumexp_to_longdt <- function(
    object,
    fvars = intersect('feature_name', autonomics::fvars(object)),
    svars = intersect('subgroup',     autonomics::svars(object)),
    assay = assayNames(object) %>% intersect(c(.[1], 'is_imputed'))
){
# Assert
    . <- sample_id <- NULL
    assert_is_valid_sumexp(object)
    assert_is_subset(fvars, autonomics::fvars(object))
    assert_is_subset(svars, autonomics::svars(object))
    svars %<>% setdiff('sample_id')
    fvars %<>% setdiff('feature_id')
    common <- intersect(svars, fvars)
    if (length(common) > 0){
        message('\t\tRemove clashing svars/fvars: ', paste0(common,collapse = ', '))
        fvars %<>% setdiff(common) # Avoid name clashes
        svars %<>% setdiff(common)
    }
# Melt
    melt <- data.table::melt.data.table
    dt <- sumexp_to_widedt(object, fvars = fvars, assay = assay[1])
    dt %<>% melt(id.vars = unique(c('feature_id', fvars)), variable.name = 'sample_id', value.name = 'value')
# Merge
    if (length(assay)>1){
        for (ass in assay[-1]){
            assdt <- sumexp_to_widedt(object, fvars = character(0), assay = ass)
            assdt %<>% melt(id.vars = 'feature_id', variable.name = 'sample_id', value.name = ass)
            dt %<>% merge(assdt, by = c('feature_id', 'sample_id'))
        }
    }
    sdt1 <- sdt(object)[, c('sample_id', svars), with = FALSE]
    dt %<>% merge(sdt1, by = 'sample_id')
    cols <- c('feature_id', fvars, 'sample_id', svars, 'value', assay[-1])
    cols %<>% unique() # avoid duplication of same fields in fid and fvars
    cols %<>% intersect(names(dt))
    dt %<>% extract(, cols, with = FALSE)
# Order and Return
    dt[, feature_id := factor(feature_id, unique(fdt(object)$feature_id))]
    dt[, sample_id  := factor(sample_id,  unique(sdt(object)$sample_id ))]
    dt[]
}


#' @export
#' @rdname sumexp_to_longdt
sumexp_to_subrep_dt <- function(object, subgroup=subgroup){
    subgroup <- enquo(subgroup)
    subgroupvar <- as_name(subgroup)

    # Assert
    assert_is_all_of(object, 'SummarizedExperiment')
    assert_is_subset(subgroupvar, svars(object))
    sample_id <- subgroup <- . <- NULL

    # Melt
    dt <- sumexp_to_longdt(object, svars = subgroupvar)
    sep <- guess_sep(object)
    dt[, replicate := stri_replace_first_fixed(
                        sample_id, dt[[subgroupvar]], '') %>%
                    substr(2, nchar(.))]

    # Partially recast
    formula <- as.formula(sprintf('feature_id + %s ~ replicate', subgroupvar))
    subrepdt <- data.table::dcast(dt, formula=formula)
    subrepdt$feature_id %<>% factor(fid_values(object))
    setorderv(subrepdt, 'feature_id')

    # Return
    subrepdt
}

#' Write sumexp to tsv
#' @param object SummarizedExperiment
#' @param assay string
#' @param file filename
#' @return NULL
#' @examples 
#' file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
#' object <- read_maxquant_proteingroups(file, fit = 'limma')
#' tsv <- file.path(tempdir(), 'fukuda20.proteingroups.tsv')
#' sumexp_to_tsv(object, file = tsv)
#' @export
sumexp_to_tsv <- function(object, assay = assayNames(object)[1], file){
    widedt <- sumexp_to_widedt(object, assay = assay)
    fwrite(widedt, file, sep = '\t')
}

#' Get fit vars/dt
#' @param object SummarizedExperimenmt
#' @return string vector
#' @examples
#' file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
#' object <- read_metabolon(file)
#' fitvars(object)
#'   fitdt(object)
#' fitvars(fit_limma(object))
#'   fitdt(fit_limma(object))
#' @export
fitvars <- function(object){
    sep <- guess_fitsep(fdt(object))
    fvars(object) %>% extract(stri_detect_fixed(., sep))
}

#' @rdname fitvars
#' @export
fitdt <- function(object){
    cols <- c('feature_id', fitvars(object))
    fdt(object)[, cols, with = FALSE]
}

#' fitcoefs
#' @param object SummarizedExperiment
#' @return string vector
#' @examples 
#' file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
#' object <- read_metabolon(file)
#' fitcoefs(object)
#' fitcoefs(fit_limma(object))
#' @export
fitcoefs <- function(object){
    sep <- guess_fitsep(fdt(object))
    if (is.null(sep))  return(NULL)
    
    fitvars(object)  %>%  
    split_extract_fixed(sep, 2:3) %>%
    unique()
}


extract_contrast_fdt <- function(object, fitcoef){ # fitcoef is needed because not all fit have same coefs
# Order
    sep <- guess_fitsep(fdt(object))
    coef <- split_extract_fixed(fitcoef, sep, 1)
    fit  <- split_extract_fixed(fitcoef, sep, 2)
    object %<>% order_on_p(coefs = coef, fit = fit)
# Extract
    allfitcols <- fvars(object) %>% extract(stri_detect_fixed(., sep))
    curfitcols <- allfitcols %>% extract(stri_detect_fixed(., fitcoef))
    annocols <- fvars(object) %>% setdiff('feature_id') %>% setdiff(allfitcols)
    cols <- c('feature_id', curfitcols, annocols)
    fdt0 <- fdt(object)[, cols, with = FALSE]
    names(fdt0) %<>% stri_replace_first_fixed(paste0(sep, coef, sep, fit), '')
    fdt0
}


#' Write xl/ods
#' @param object  SummarizedExperiment
#' @param xlfile  file
#' @param odsfile file
#' @param fitcoefs character vector
#' @return filepath
#' @examples 
#' file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
#' object <- read_metabolon(file, fit = 'limma')
#' xlfile  <- file.path(tempdir(), 'fukuda20.proteingroups.fdt.xlsx')
#' odsfile <- file.path(tempdir(), 'fukuda20.proteingroups.fdt.ods')
#' # write_xl(object,  xlfile)
#' # write_ods(object, odsfile)
#' @export
write_xl <- function(
    object, xlfile, fitcoefs = autonomics::fitcoefs(object)
){
# Assert
    if (!requireNamespace('writexl', quietly = TRUE)){
        message("`BiocManager::install('readxl')`. Then re-run.")
        return(NULL)
    }
    assert_is_valid_sumexp(object)
    assert_all_are_dirs(dirname(xlfile))
# Write
    fdt(object) %<>% add_adjusted_pvalues('fdr')
    list0 <- mapply(extract_contrast_fdt, fitcoef = fitcoefs, MoreArgs = list(object = object), SIMPLIFY = FALSE)
    writexl::write_xlsx(list0, path = xlfile)
# Return
    return(xlfile)
}


#' @rdname write_xl
#' @export
write_ods <- function(
    object, odsfile, fitcoefs = autonomics::fitcoefs(object)
){
# Assert
    if (!requireNamespace('readODS', quietly = TRUE)){
        message("`BiocManager::install('readODS')`. Then re-run.")
        return(NULL)
    }
    assert_is_valid_sumexp(object)
    assert_all_are_dirs(dirname(odsfile))
# Prepare    
    fdt(object) %<>% add_adjusted_pvalues('fdr')                             # add fdr
    list0 <- mapply(extract_contrast_fdt, fitcoef = fitcoefs,                # extract contrastfdt
                                         MoreArgs = list(object = object), 
                                         SIMPLIFY = FALSE)
    if (file.exists(odsfile))  unlink(odsfile)                               # rm old file
# Write
    readODS::write_ods(list0[[1]], sheet = names(list0)[[1]],                # write first sheet (has to be done first)
                                    path = odsfile)
    if (length(list0)==1)  return(odsfile)
    mapply(readODS::write_ods, x = list0[-1],                                # then append other sheets
                           sheet = names(list0[-1]), 
                        MoreArgs = list(path = odsfile, 
                                      append = TRUE), 
                        SIMPLIFY = FALSE)
    return(odsfile)
}


#' `data.table` to `matrix`
#'
#' Convert between `data.table` and `matrix`
#'
#' @param x  data.table / matrix
#' @param idvar idvar string
#' @return matrix / data.table
#' @examples
#' x <- data.table::data.table(
#'         gene    = c('ENSG001', 'ENSG002', 'ENSG003'),
#'         sampleA = c(1787, 10, 432),
#'         sampleB = c(1143,  3, 268))
#' dt2mat(x)
#' mat2dt(dt2mat(x), 'gene')
#' @export
dt2mat    <- function(x) x[,-1] %>% as.matrix() %>% set_rownames(x[[1]])


#' @rdname dt2mat
#' @export
mat2dt    <- function(x, idvar){
                . <- NULL
                x %<>% data.table(keep.rownames = TRUE)
                names(x)  %<>% gsub('rn', idvar, .,  fixed = TRUE)
                x }

dt2DF     <- function(dt) DataFrame(dt, row.names = dt[[1]])
dt2exprs  <- function(dt) dt2mat(data.table::dcast(
                            dt, feature_id ~ sample_id, value.var = 'value'))
dt2sumexp  <- function(
    dt,
    fvars = character(0),
    svars = setdiff(names(dt), c('feature_id', fvars, 'sample_id', 'value'))
){
    exprs1 <- dt2exprs(dt)
    sdata1 <- dt2DF(dt[, .SD[1], by = 'sample_id' ])[, c('sample_id',  svars),
                                                        drop = FALSE ]
    fdata1 <- dt2DF(dt[, .SD[1], by = 'feature_id'])[, c('feature_id', fvars),
                                                        drop = FALSE ]
    SummarizedExperiment(
        assays = list(exprs = exprs1),
        rowData = fdata1,
        colData = sdata1)
}


#' Convert matrix into SummarizedExperiment
#' @param x             matrix
#' @param verbose       TRUE/FALSE
#' @return SummarizedExperiment
#' @examples
#' file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
#' x <- values(read_metabolon(file))
#' object <- matrix2sumexp(x)
#' object %<>% pca()
#' biplot(object, color = 'subgroup')
#' @export
matrix2sumexp <- function(x, verbose = TRUE){
    object <- SummarizedExperiment(list(exprs = x))
    fdata(object)$feature_id   <- rownames(object)
    sdata(object)$sample_id    <- colnames(object)
    object %<>% add_subgroup(verbose = verbose)
    object
}