shinyGenePlot: Shiny genePlot Widget

In ZachHunter/bvt: Visualization Tools for Bioconductor

Shiny genePlot Widget

Description

A shiny widget for bvt's genePlot

Usage

shinyGenePlot(
  data,
  geneList,
  factorList,
  gpOptions,
  dbName = "data",
  themeName = "basicTheme"
)

Arguments

data	ExpressionSet or other R data object containing the data and possibly feature or phenotype information. While intended for use with Bioconductor objects, data.frame, matrix, and tibble can also be used.
geneList	character vector; List of all possible gene names including expression data row names and gene symbols if in use.
factorList	all possible factors from phenotype data.
gpOptions	active options from the command line.
dbName	character; Name of the database passed to genePlot. If using the iris data set this should be set to "iris".
themeName	character; Name of of the selected npTheme as a character string. Used to set the default value in shiny. As eval and parse are used to access the theme settings any npTheme object in the enviroment will do, including custom themes.

Details

This is a the optional gui interface for using genePlot. It is an internal function that is not exported The interface returns the options selected by the user. The GUI allows for extensive customization and returns the effective plotting command and npData object for plotting. This is due to the way that RStudio handles graphics a and seems to have issues with immediately ploting the data. For this reason the data is plotted in base R but only the npData object is returned in RStudio. This can to plotted using plot or genePlot or any nicePlots function.

See Also

genePlot

Examples

ToDo<-1

ZachHunter/bvt documentation built on Sept. 18, 2024, 3:12 p.m.