reportAnnotation: Specialized report functions

Description

Functions that provide a html report of genetic interactions screens for specific topics.

Usage

reportAnnotation        (sgi, verbose = 0, path = ".", dir = "annotation", prefix = "annotation", report = NULL)
reportStatistics        (sgi, verbose = 0, path = ".", dir = "stats",
			 prefix = "stat", report = NULL)
reportGeneLists         (sgi, verbose = 0, path = ".", dir = "hitlist", 
			 prefix = "hitlist", report = NULL)
reportNetworks          (sgi, verbose = 0, path = ".", dir = "networks",
			 prefix = "networks", Networks, qv = 0.05,
			 withoutgroups = c("pos", "neg"), report = NULL)
reportScreenData        (sgi, type = "data", design = "template",
			 do.trafo = TRUE, do.inv.trafo = FALSE, verbose = 0, 			 path = ".", dir = "screenplots", prefix = "screenplot",
			 png.args = list(width = 960, height = 960),
			 pdf.args = list(width = 7, height = 7),
			 plotScreen.args = list(ncol = 6L, do.legend = TRUE,
			                        fill = c("red", "white", "blue")),
			 png.scatter.args = list(width = 400, height = 400),
			 pdf.scatter.args = list(width = 7, height = 7), report = NULL)
reportDoublePerturbation(sgi, verbose = 0, path = ".", dir = "doublePerturbations",
			 prefix = "doublePerturbationPlots", report = NULL, withoutgroups = c("neg", "pos"), png.args = list(width = 500, height = 500),
			 pdf.args = list(width = 7, height = 7), ...)
reportMainEffects       (sgi, verbose = 0, path = ".", dir = "maineffects",
			 prefix = "maineffects",
			 png.args = list(width = 500, height = 500),	
			 pdf.args = list(width = 7, height = 7),
			 plot.args = list(), report = NULL)
reportHeatmap           (sgi, verbose = 0, path = ".", dir = "heatmap",
			 prefix = "heatmap",
			 png.args = list(width = 1000, height = 1000),
			 pdf.args = list(width = 15, height = 15),
			 report = NULL, withoutgroups = c("neg", "pos"))

Arguments

sgi

An object of class RNAinteract.

verbose

Either 0 (default, no output), 1 (minimum output), or 2 (outout)

path

The main path to the HTML report directory.

dir

A subdirectory where the report is written to.

prefix

A prefix for each file written in the subdirectory. Using different prefixes, one can write multiple reports in the same directory.

report

A report object as generated by startReport.

Networks

A boolean array with edges from interaction graphs.

A cut-off value for the q-values.

withoutgroups

Genes annotated with these groups are not plotted in this report.

type

Any "type" that can be passed to getData.

design

Either "template" (default) or "query"

do.trafo, do.inv.trafo

Apply the (inverse) transformation before plotting.

png.args

A list with entries width and height specifying the width and height of the generated png images.

pdf.args

A list with entries width and height specifying the width and height of the generated of files.

plotScreen.args

Arguments for the screen plots

png.scatter.args, pdf.scatter.args, plot.args

Arguments for the scatter plots

...

Parameters passed to the plotting functions.

Value

All functions return a report object as returned by startReport.

Details

Each of these function generates a HTML report. It is added to a HTML frame.

The report object has to be created with startReport beforehand. Multiple report functions can be called afterwards. When all reports are written, the report is finalized and closed by endReport.

Examples

Run this code

data("sgi")
report = startReport("report")
reportAnnotation(sgi, report = report)
endReport(report)
# browseURL(file.path("report","index.html"))

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