grandR (version 0.2.6)

ServeGrandR: Serve a shiny web interface

Description

Fire up a shiny web server for exploratory analysis of grandR data.

Usage

ServeGrandR(
  data,
  table = NULL,
  sizes = NA,
  height = 400,
  floating.size = c(350, 350),
  plot.gene = NULL,
  plot.global = NULL,
  plot.window = NULL,
  highlight = NULL,
  df.identifier = "Symbol",
  title = Title(data),
  show.sessionInfo = FALSE,
  help = list(".Q: multiple testing corrected p values", ".LFC: log2 fold changes")
)

Value

a shiny web server

Arguments

data

the grandR object (or a file name to an rds file containing a grandR object)

table

the table to display (can be NULL or a named list; see details)

sizes

the widths for the gene plots to show (12 is full screen with); must be a vector as long as there are gene plots

height

the height for the gene plots in pixel

floating.size

either a vector (width,height) for all plots in floating windows or a named list of such vectors for each floating window

plot.gene

a list of gene plots; can be NULL, then the stored gene plots are used (see Plots)

plot.global

a list of global plots; can be NULL, then the stored global plots are used (see Plots)

plot.window

a list of static plots to show in a floating window; see details

highlight

a vector of gene names that are highlighted in the beginning; can also be a column name in the (first) table

df.identifier

the main identifier (column name) from the table; this is used when calling the gene plot functions;

title

the title to show in the header of the website

show.sessionInfo

whether to show session info

help

a list of characters that is shown as help text at the beginning (when no gene plot is shown); should describe the contents of your table

Details

If the table parameter is NULL, either an analysis table named "ServeGrandR" is used (if it exists), otherwise the columns "Q", "LFC", "Synthesis" and "Half-life" of all analysis tables are used. If it is a list, a menu is created in the navbar

plot.window must be a list of plotting functions that receive the grandR object and return a plot. It can also be a list of list, in which case more than one plotting windows are generated. Each plot will be rendered with a size of 350x350.

The gene plots must be functions that accept two parameters: the grandR object and a gene identifier. You can either use functions directly (e.g. plot.gene=list(PlotGeneOldVsNew)), or use Defer in cases you need to specify additional parameters, e.g. plot.gene=list(Defer(PlotGeneOldVsNew,log=FALSE)). The global plots are functions accepting a single parameter (the grandR object). Here the use of Defer is encouraged due to its caching mechanism.

Examples

if (FALSE) {
sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Condition",Design$dur.4sU,Design$Replicate))
sars <- Normalize(sars)
sars <- Pairwise(sars,contrasts = GetContrasts(sars,contrast = c("Condition","SARS","Mock")))
sars <- AddGenePlot(sars,"timecourse",
                    Defer(PlotGeneProgressiveTimecourse,steady.state=c(Mock=TRUE,SARS=FALSE)))
sars <- AddGlobalPlot(sars,"Vulcano",VulcanoPlot)
ServeGrandR(sars)

}