makeShinyFiles: Generate data files required for shiny app

In SGDDNB/ShinyCell: Shiny Interactive Web Apps for Single-Cell Data

Generate data files required for shiny app

Description

Generate data files required for shiny app. Five files will be generated, namely (i) the shinycell config prefix_conf.rds, (ii) the gene mapping object config prefix_gene.rds, (iii) the single-cell gene expression prefix_gexpr.h5, (iv) the single-cell metadata prefix_meta.rds and (v) the defaults for the Shiny app prefix_def.rds. A prefix is specified in each file to allow for the use of multiple single-cell datasets in one Shiny app. Note that both makeShinyFiles and makeShinyCodes functions are ran when running the wrapper function makeShinyApp.

Usage

makeShinyFiles(
  obj,
  scConf,
  gex.assay = NA,
  gex.slot = c("data", "scale.data", "counts"),
  gene.mapping = FALSE,
  shiny.prefix = "sc1",
  shiny.dir = "shinyApp/",
  default.gene1 = NA,
  default.gene2 = NA,
  default.multigene = NA,
  default.dimred = NA,
  chunkSize = 500
)

Arguments

obj	input single-cell object for Seurat (v3+) / SingleCellExperiment data or input file path for h5ad / loom files
scConf	shinycell config data.table
gex.assay	assay in single-cell data object to use for plotting gene expression, which must match one of the following: Seurat objects: "RNA" or "integrated" assay, default is "RNA" SCE objects: "logcounts" or "normcounts" or "counts", default is "logcounts" h5ad files: "X" or any assay in "layers", default is "X" loom files: "matrix" or any assay in "layers", default is "matrix"
gex.slot	slot in single-cell assay to plot. This is only used for Seurat objects (v3+). Default is to use the "data" slot
gene.mapping	specifies whether to convert human / mouse Ensembl gene IDs (e.g. ENSG000xxx / ENSMUSG000xxx) into "user-friendly" gene symbols. Set this to TRUE if you are using Ensembl gene IDs. Default is FALSE which is not to perform any conversion. Alternatively, users can supply a named vector where names(gene.mapping) correspond to the actual gene identifiers in the gene expression matrix and gene.mapping correspond to new identifiers to map to
shiny.prefix	specify file prefix
shiny.dir	specify directory to create the shiny app in
default.gene1	specify primary default gene to show
default.gene2	specify secondary default gene to show
default.multigene	character vector specifying default genes to show in bubbleplot / heatmap
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(s)

John F. Ouyang

Examples

makeShinyFiles(seu, scConf, gex.assay = "RNA", gex.slot = "data",
               shiny.prefix = "sc1", shiny.dir = "shinyApp/",
               default.gene1 = "GATA3", default.gene2 = "DNMT3L",
               default.multigene = c("ANPEP","NANOG","ZIC2","NLGN4X","DNMT3L",
                                     "DPPA5","SLC7A2","GATA3","KRT19"),
               default.dimred = c("UMAP_1", "UMAP_2"))

SGDDNB/ShinyCell documentation built on Jan. 25, 2024, 3:19 p.m.