makeShinyApp: Make a shiny app
In SGDDNB/ShinyCell: Shiny Interactive Web Apps for Single-Cell Data

makeShinyApp

R Documentation

Make a shiny app

Description

Make a shiny app based on the shinycell config data.table and single-cell data object.

Usage

makeShinyApp(
  obj,
  scConf,
  gex.assay = NA,
  gex.slot = c("data", "scale.data", "counts"),
  gene.mapping = FALSE,
  shiny.title = "scRNA-seq shiny app",
  shiny.footnotes = "",
  shiny.dir = "shinyApp/",
  enableSubset = TRUE,
  defPtSiz = 1.25,
  ganalytics = NA,
  default.gene1 = NA,
  default.gene2 = NA,
  default.multigene = NA,
  default.dimred = NA
)

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.title`	title for shiny app
`shiny.footnotes`	text for shiny app footnote. When given as a list, citation can be inserted by specifying author, title, journal, volume, page, year, doi, link. See example below.
`shiny.dir`	specify directory to create the shiny app in. Default is to create a new directory named "shinyApp"
`enableSubset`	specify whether to enable "Toggle to subset cells" functionality in the shiny app. Default is to enable this functionality
`defPtSiz`	specify default point size for single cells. For example, a smaller size can be used if you have many cells in your dataset
`ganalytics`	Google analytics tracking ID (e.g. "UA-123456789-0")
`default.gene1`	specify primary default gene to show
`default.gene2`	specify secondary default gene to show
`default.multigene`	character vector specifying the 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

Value

directory containing shiny app

Author(s)

John F. Ouyang

Examples

# Example citation
citation = list(
  author  = "Liu X., Ouyang J.F., Rossello F.J. et al.",
  title   = "",
  journal = "Nature",
  volume  = "586",
  page    = "101-107",
  year    = "2020", 
  doi     = "10.1038/s41586-020-2734-6",
  link    = "https://www.nature.com/articles/s41586-020-2734-6")
makeShinyApp(seu, scConf, 
             shiny.title = "scRNA-seq Shiny app",
             shiny.dir = "shinyApp/", shiny.footnotes = citation,
             default.gene1 = "NANOG", 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.