pipe.TranscriptToHTML: Turn transcriptome into HTML table with gene plot hyperlinks.

Usage Arguments Details Value Author(s) See Also

Usage

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pipe.TranscriptToHTML(sampleID, speciesID = NULL, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", results.path = NULL, N = 100, minYmax = 10, 
	tailWidth = 1000, pause = NULL, altGeneMap = NULL, altGeneMapLabel = NULL, 
	targetID = NULL, plotType = "box", useLog = FALSE, label = "", 
	PLOT.FUN = NULL, geneSet = NULL, ...)

Arguments

sampleID

the SampleID for this sample. This SampleID keys for a row of annotation details in the annotation file, for getting sample-specific details. The SampleID is also used as a sample-specific prefix for all files created during the processing of this sample.

speciesID

The SpeciesID of the target species to operate on. By default, all species in the current target are turned into HTML tables.

annotationFile

the file of sample annotation details, which specifies all needed sample-specific information about the samples under study. See DuffyNGS_Annotation.

optionsFile

the file of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.

results.path

The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.

N

The number of genes to include in the HTML table, and make gene plot images for.

minYmax

Plotting option passed to low level default gene plot function, sets the lowest maximum Y axis limit. Useful for making low and high expressing genes share similar plot bounds.

tailWidth

Plotting option passed to low level default gene plot function, sets the extent of intergenic space outside the gene boundaries to include in the plot, to enlarge the X axis limits. Useful for seeing the genomic neighborhood around genes. Units are in nucleotides.

plotType

Plotting option passed to low level default gene plot function, controls the type of read pileup images generated. May be one of "boxes" for color-filled boxes, "lines" for colored lines, and "segments" for colored line segments.

useLog

logical, should the Y axis be shown as log scaled.

altGeneMap

An alternate data frame of gene annotations, in a format identical to getCurrentGeneMap, that has the gene names and locations to be measured for read pileup depth. By default, use the standard built-in gene map for each species.

altGeneMapLabel

A character string identifier for the alternate gene map, that becomes part of all created path and file names to indicate the gene map that produced those transcriptomes.

label

optional text to append as part of the "main" plot legend.

PLOT.FUN

the name of an optional function to call instead of the default read pileups function. Only requirement is the that the first argument be the name of the gene to be drawn.

geneSet

an optional character vector of GeneIDs, that limits the HTML table to only include genes in this set.

...

other arguments passed down to the low level gene plotting function.

Details

This is an optional pipeline tool to convert static transcriptome results into more interactive HTML. Writes files and gene plot images to the html subfolder under the main results path. Including too many genes makes for unresponsive HTML and overly large plot folders, so use discretion with "N".

Value

Writes HTML files and hyperlinked gene plot images to the htlm subfolder.

Author(s)

Bob Morrison

See Also

pipe.Transcriptome for creating transcriptome files from BAM files. pipe.PlotGene for making default gene plot images. table2html for the low level tool that turns data frames to HTML.


robertdouglasmorrison/DuffyNGS documentation built on Dec. 7, 2018, 8:01 a.m.