tsvtogginp: Convert a single sequence's quasi-standard TSV "row" input...

In vragh/seqvisr: Biological Sequence Visualization and Auxiliary Functions in R

Convert a single sequence's quasi-standard TSV "row" input data.frame format to a position-per-row ggplot()-friendly format.

Description

Convert a single sequence's quasi-standard TSV "row" input data.frame format to a position-per-row ggplot()-friendly format.

Usage

tsvtogginp(inpdf = NULL)

Arguments

inpdf

(character, mandatory) the name of the input data.frame().

Details

Function to take a data.frame() indicating the sequence name, length, sequence start offset, feature height, feature color, and feature start and end positions (one row for each feature), FOR ONE SEQUENCE, and convert this into (another) data.frame that can be parsed by ggplot2. Namely, the output data.frame has one row for each residue in the sequence, and indicates the positions (important for ggplot2), and the associated annotation (e.g., "ABC domain"). The function also has additional columns indicating data for labeling that should be visualized on the plot or used to create it–this is basically done by taking the feature's name and assigning it to a label column but only for a single residue at the middle of the feature. (If the labels of all residues from each feature are displayed, the labeling will be illegible.)

tsvtogginp() is invoked by pdomvisr() through the wrapper script tsvtgginp_multi().

Value

a data.frame() with one row per residue indicating the sequence name, position (indicated by that row), the description associated with that position (e.g., "ABC domain", or NA for no description), a column indicating which feature the position belongs to (e.g., say there are two domains named "ABC", this numerical column is a way to distinguish between them), a column indicating the layer (offset, base, feature; see ?pdomvisr()), a numerical column indicating the height for the feature's tiles, an alphanumeric column indicating the colors assigned to the item's tiles, labels for the particular feature (assigned to one position within the feature; see ?pdomvisr()), and a column indicating the original positions of the rows (e.g., when a sequence offset has been applied; see ?pdomvisr()). Column names are: prot_acc, pos, posdesc, fset, layer, height, color, label, orig_pos.

See Also

tsvtogginp_multi(), pdomvisr()

Examples

## Not run: 
#Input data
inpath <- system.file("extdata", "pdomvisr_testdata.tsv", package = "seqvisr", mustWork = TRUE)
inpdat <- read.table(inpath, header = TRUE)
inpdat <- inpdat[2:3, ]

#Example run
tsvtogginp(inpdat)

## End(Not run)

vragh/seqvisr documentation built on April 20, 2024, 10:06 a.m.