R/multimodal-wrapper.R

In ajabadi/BIRSBIO2020.scNMTseq.PLS: scNMTseq challenge analysis using a PLS approach

#' MuliModalSparsePLS(DA)
#'
#' @param mae A MultiAssayExperiment object
#' @param study_assays study assays. first must be 'rna' for unsupervised analysis
#' @param lineages Character, lineages to keep, from unique(colData(mae)$lineage10x_2)
#' @param stages Character, stages to keep, from unique(colData(mae)$stage)
#' @param ncomp Integer, number of components
#' @param scale Logical, whether to scale the features
#' @param DA NULL for unsupervised, or from names(colData(mae)) for supervised (PLSDA)
#' @export
multimodal_sPLS_wrapper <- function(mae, study_assays, lineages=NULL, stages = NULL, ncomp = 2, scale = TRUE, design = 'null', DA=NULL, keepX = NULL, save = TRUE) {

  if (is.null(study_assays)) {
    study_assays <- names(experiments(mae))
    study_assays <- study_assays[!grepl(pattern = '^wt_*', x = study_assays)]
  }
  if (is.integer(study_assays)) {
    study_assays <- names(experiments(mae))[study_assays]
  }
  mae <- mae[,,study_assays]
  mae <- mixOmics::make_unique_feature_names(mae)
  if (!is.null(lineages)) {
    mae <- mae[,mae$lineage10x_2 %in% lineages,]
    lin <- 'AllLineages'
  } else{
    lineages <- unique(mae$lineage10x_2 )
    lin <- paste0(lineages, collapse = '-')
  }

  if (is.null(stages)) {
    stages <- unique(mae$stage)
  }

  stag <- paste(stages, collapse = '-')
  mae <- mae[,mae$stage %in% stages,]

  if (is.null(keepX)) {
    keepX <- lapply(named_list(study_assays), function(z){
      p <- dim(assay(mae, z))[1]
      keepx <- ifelse(p > 500, 50, max(25, ceiling(p/10)))
      rep(keepx, ncomp)
    })
  }
  if (!is.null(DA)) {
    pls_mode = 'PLSDA'
    formu <- as.formula(sprintf('%s ~ %s', DA, paste(study_assays, collapse = ' + ')))
    out <- MultiModalSparsePLSDA(data = mae, formula = formu, keep_features = keepX, ncomp = ncomp, design = design, scale = scale)
  } else {
    if (study_assays[1] != 'rna') {
      stop('First assay should be "rna"')
    }
    pls_mode = 'PLS'
    formu <- as.formula(sprintf('rna ~ %s', paste(study_assays[-1], collapse = ' + ')))
    out <- MultiModalSparsePLS(data = mae, formula = formu, keep_features = keepX, ncomp = ncomp, design = design, scale = scale)
  }
  NAME <- sprintf('savedata/MultiModalSparse%s_%s__%s__%s__%s.rds', pls_mode, ifelse(is.null(DA), 'rna', DA), paste0(study_assays[-1], collapse = '-'), lin, stag)


  if (isTRUE(save)) {
    saveRDS(out, file = NAME)
  }
  out
}