added new check for module eigengenes

Package: hdWGCNA

Title: WGCNA

Version: 0.1.1.9001

Title: hdWGCNA

Version: 0.1.1.9002

Authors@R: c(

    person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),

           comment = c(ORCID = "0000-0002-7768-4856")),

# hdWGCNA 0.1.1.9002 (2022-5-24)

## Added

- `ModuleEigengenes` checks to make sure the data has been scaled.

## Changes

- None

# hdWGCNA 0.1.1.9001 (2022-05-09)

## Added

- Wrote docstring for `PlotKMEs` so it would actually be included in the package.

    multiExpr <- GetMultiExpr(seurat_obj)

    checkSets(multiExpr) # check data size

    print('here')

  # constructing network on a single dataset

  } else{

  if(!dir.exists(tom_outdir)){

    dir.create(tom_outdir)

  }

  print('here')

  if(is.null(soft_power) & !consensus){

    soft_power <- GetPowerTable(seurat_obj) %>% subset(SFT.R.sq >= 0.8) %>% .$Power %>% min

    cat(paste0("Soft power not provided. Automatically using the lowest power that meets 0.8 scale-free topology fit. Using soft_power = ", soft_power, "\n"))

  } else if(consensus){

  } else if(is.null(soft_power)){

    power_tables <- GetPowerTable(seurat_obj) %>% dplyr::group_split(group)

    soft_power <- sapply(power_tables, function(power_table){

      power_table %>% subset(SFT.R.sq >= 0.8) %>% .$Power %>% min

    })

    cat(paste0("Soft power not provided. Automatically using the lowest power that meets 0.8 scale-free topology fit. Using soft_power = c(", paste0(soft_power, collapse=','), ")\n"))

  }

  print('here')

  # construct the network

  net <- WGCNA::blockwiseConsensusModules(

  # are we going to run Harmony?

  harmonized = !is.null(group.by.vars)

  if(harmonized & !any(grepl("ScaleData", seurat_obj@commands))){

      stop('Need to run ScaleData before running ModuleEigengenes with group.by.vars option.')

  }

  me_list <- list()

  harmonized_me_list <- list()

  group.by.vars=NULL,

  gene_mapping=NULL, # table mapping genes from species 1 to species 2

  genome1_col=NULL, genome2_col=NULL,

  scale_genes = FALSE,

  vars.to.regress = NULL,

  scale.model.use = 'linear',

  wgcna_name=NULL, wgcna_name_proj=NULL,

  ...

){

    counts = new_exprs

  )

  print('here')

  print(meta)

  print(names(meta))

    stop('Invalid character # found in group.by, please re-name the group.')

  }

  if(!(ident.group %in% group.by)){

    stop('ident.group must be in group.by')

  }

  # subset seurat object by seleted cells:

  if(!is.null(cells.use)){

    seurat_full <- seurat_obj

    MoreArgs = list(k=k, reduction=reduction, assay=assay, slot=slot, return_metacell=TRUE, wgcna_name=wgcna_name)

  )

  names(metacell_list) <- groupings

  print('done making metacells')

  # combine metacell objects

  metacell_obj <- merge(metacell_list[[1]], metacell_list[2:length(metacell_list)])

  print('done merging seurat objc')

  # set idents for metacell object:

  Idents(metacell_obj) <- metacell_obj@meta.data[[ident.group]]

  print('set idents')

  # revert to full seurat object if we subsetted earlier

  if(!is.null(cells.use)){

  # add seurat metacell object to the main seurat object:

  seurat_obj <- SetMetacellObject(seurat_obj, metacell_obj, wgcna_name)

  print('update seurat')

  # add other info

  seurat_obj <- SetWGCNAParams(

    ),

    wgcna_name

  )

  print('set params')

  seurat_obj

}

      </button>

      <span class="navbar-brand">

        <a class="navbar-link" href="https://smorabit.github.io/scWGCNA/index.html">hdWGCNA</a>

        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9001</span>

        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9002</span>

      </span>

    </div>