projectmodules update

Package: hdWGCNA

Title: hdWGCNA

Version: 0.1.1.9010

Version: 0.1.1.9011

Authors@R: c(

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

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

# hdWGCNA 0.1.1.9009 (2022-07-30)

# hdWGCNA 0.1.1.9011 (2022-08-17)

## Added

- None

## Changes

- Reverted the `exclude_grey` flag back to doing nothing in the `ModuleEigengenes` function because it messed up some downstream tasks, will resolve in a future update.

- `ProjectModules` now excludes modules with too many missing genes in the query dataset,

tunable by the `overlap_proportion` parameter.

# hdWGCNA 0.1.1.9010 (2022-07-30)

## Added

- None

  group.by.vars=NULL,

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

  genome1_col=NULL, genome2_col=NULL,

  overlap_proportion = 0.5,

  vars.to.regress = NULL,

  scale.model.use = 'linear',

  wgcna_name=NULL, wgcna_name_proj=NULL,

    modules <- TransferModuleGenome(modules, gene_mapping, genome1_col, genome2_col)

  }

  # what is the proportion of genes in each module that are in seurat_obj?

  mods <- as.character(unique(modules$module))

  mod_props <- unlist(lapply(mods, function(x){

    cur_mod <- subset(modules, module == x)

    sum(cur_mod$gene_name %in% rownames(seurat_obj)) / nrow(cur_mod)

  }))

  mods_keep <- mods[mod_props >= overlap_proportion]

  # only keep modules that have enough overlapping genes

  modules <- subset(modules, module %in% mods_keep) %>%

    dplyr::mutate(module = droplevels(module))

  # get genes that overlap between WGCNA genes & seurat_obj genes:

  gene_names <- modules$gene_name

  genes_use <- intersect(gene_names, rownames(seurat_obj))

      this_choice <- cell_sample[nrow(cell_sample), ]

      shared <- sapply(others, get_shared, this_choice = this_choice)

      # if (max(shared) < 0.9 * k) { # old way of doing it

      if(max(shared) <= max_shared){

          chosen <- new_chosen

      }

      </button>

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        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9010</span>

        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.1.1.9011</span>

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