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Generate code files required for shiny app

Source: R/makeShinyCodes.R
makeShinyCodes.Rd

Generate code files required for shiny app for both single-dataset and multi-dataset scenarios. Specifically, two R scripts will be generated, namely server.R and ui.R. Note that makeShinyFiles has to be ran prior to make the necessary data files for each dataset included. The prefix used in makeShinyFiles have to be then supplied in this function.

Usage

makeShinyCodes(
  shiny.title,
  shiny.footnotes = "",
  shiny.prefix,
  shiny.headers,
  shiny.dir,
  defPtSiz = 1.25,
  ganalytics = NA
)

Arguments

shiny.title

specify the overall 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.prefix

specify file prefix for each dataset. Must match the prefix used in makeShinyFiles

shiny.headers

specify the tab header names for each dataset. Length must match that of shiny.prefix. Note that this is ignored if there is only one dataset

shiny.dir

specify directory to create the shiny app in

defPtSiz

specify default point size for single cells. For example, a smaller size can be used if you have many cells in your dataset. A single value can be specified to set the point size for all datasets. Otherwise, users have to specify one value for each dataset

ganalytics

Google analytics tracking ID (e.g. "UA-123456789-0")

Value

server.R and ui.R required for shiny app

Details

The three output files (server.R, ui.R, shinyFunc.R) are assembled from jinjar templates shipped under inst/templates. The master templates (server.R.jinja, ui.R.jinja, shinyFunc.R.jinja) contain the orchestration logic - which tab blocks to include for each dataset, gated on the presence of spatial / ATAC / DEG data - and {% include %} one partial per tab block. All per-dataset facts (prefix, headers, point sizes, spatial slider parameters and which data types are present) are computed here in R and passed as the template context.

Author

John F. Ouyang

Examples

if (FALSE) { # \dontrun{
# 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")
makeShinyCodes(shiny.title = "scRNA-seq shiny app", shiny.footnotes = "",
               shiny.prefix = c("sc1", "sc2"), defPtSiz = c(1.25, 1.5),
               shiny.headers = c("dataset1", "dataset2"),
               shiny.dir = "shinyApp/")
} # }