Generate data files required for shiny app (ArchR object)

Generate data files required for shiny app, specifically scATAC-seq data Six files will be generated, namely (i) the CellSight config prefix_conf.rds, (ii) the single-cell metadata prefix_meta.rds, (iii) the single-cell assays prefix_assay_X.h5, (iv) the feature mapping object config prefix_gene.rds, (v) the dimension reduction embeddings prefix_dimr.rds and (vi) the defaults for the Shiny app prefix_def.rds and (vii) the bigwig files for trackplot prefix_bw_GRP. A prefix is specified for each set of files to allow for multiple single-cell datasets in a single Shiny app.

Usage

makeShinyFilesATACarchr(
  obj,
  scConf,
  bigWigGroup = NA,
  assay = NA,
  dimred.to.use = NA,
  shiny.prefix = "sc1",
  shiny.dir = "shinyApp/",
  default.gene1 = NA,
  default.gene2 = NA,
  default.multigene = NA,
  default.dimred = NA,
  ...
)

Arguments

obj

input ArhcR object

scConf

CellSight config data.table

bigWigGroup

categorical group in ArhcR meta.data to group cells by for the generation of bigWig files for track plot. Default is NA which does not generate any bigWig files.

assay

assay(s) in ArhcR object to use. Multiple assays can now be incorporated and all assays are used by default (with the first assay being the default assay), which must match one of the following:

• ArchR objects: "TileMatrix" or "GeneScoreMatrix" or "GeneIntegrationMatrix" or "PeakMatrix" or "MotifMatrix", default is "PeakMatrix"

dimred.to.use

specify the dimension reduction to use. Default is to use all except LSI

shiny.prefix

specify file prefix

shiny.dir

specify directory to create the shiny app in

default.gene1

specify primary default feature (peak or gene or TF) to show, which must be present in the default assay

default.gene2

specify secondary default feature (peak or gene or TF) to show, which must be present in the default assay

default.multigene

character vector specifying default features to show in bubbleplot / heatmap, which be present in the default assay

default.dimred

character vector specifying the two default dimension reductions. Default is to use UMAP if not TSNE embeddings

...

extra arguments to supply to ArchR::getGroupBW

Value

data files required for shiny app

Author

John F. Ouyang

Examples

if (FALSE) { # \dontrun{
makeShinyFilesATACarchr(ArchR, scConf, 
                        shiny.prefix = "sc1", shiny.dir = "shinyApp/")
} # }