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

Usage

ServeGrandR(
  data,
  table = NULL,
  sizes = NA,
  height = 400,
  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")
)

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

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

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

Value

a shiny web server

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)

}