reportAnnotation: Specialized report functions

In RNAinteract: Estimate Pairwise Interactions from multidimensional features

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.
qv	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.

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.

Value

All functions return a report object as returned by startReport.

Author(s)

Bernd Fischer

See Also

RNAinteract-package, startReport, endReport

Examples

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

RNAinteract documentation built on Nov. 8, 2020, 5:28 p.m.