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Generate data files required for shiny app (scRNA type data)

Source: R/makeShinyFilesGEX.R
makeShinyFilesGEX.Rd

Generate data files required for shiny app, specifically scRNA-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. A prefix is specified for each set of files to allow for multiple single-cell datasets in a single Shiny app.

Usage

makeShinyFilesGEX(
  obj,
  scConf,
  gex.assay = NA,
  gex.slot = "data",
  dimred.to.use = NA,
  shiny.prefix = "sc1",
  shiny.dir = "shinyApp/",
  default.gene1 = NA,
  default.gene2 = NA,
  default.multigene = NA,
  default.dimred = NA,
  chunkSize = 500
)

Arguments

obj

input Seurat (v3+) object or input file path for h5ad file

scConf

CellSight config data.table

gex.assay

assay(s) in single-cell data 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:

  • Seurat objects: "RNA" or "integrated" assay, default is "RNA"

  • h5ad files: "X" or any assay in "layers", default is "X"

gex.slot

slot in single-cell assay to plot. This is only used for Seurat objects (v3+). Default is to use the "data" slot

dimred.to.use

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

shiny.prefix

specify file prefix

shiny.dir

specify directory to create the shiny app in

default.gene1

specify primary default gene to show, which be present in the default assay for Seurat or X layer in scanpy h5ad

default.gene2

specify secondary default gene to show, which be present in the default assay for Seurat or X layer in scanpy h5ad

default.multigene

character vector specifying default genes to show in bubbleplot / heatmap, which be present in the default assay for Seurat or X layer in scanpy h5ad

default.dimred

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

chunkSize

number of genes written to h5file at any one time. Lower this number to reduce memory consumption. Should not be less than 10

Value

data files required for shiny app

Author

John F. Ouyang

Examples

if (FALSE) { # \dontrun{
makeShinyFilesGEX(seu, scConf, shiny.prefix = "sc1", shiny.dir = "shinyApp/",
                  default.gene1 = "POU5F1", default.gene2 = "APOA1",
                  default.multigene = c("POU5F1","APOA1","GPRC5A","TBXT","ISL1"),
                  default.dimred = "umap")
} # }