pixelgram: pixelgram: Display a pixel plot and phylogram of aligned...

In phraber/pixelgram: Pixel View with Accompanying Phylogram of Sequence Alignment

Description

The two principal methods are aconstructor, which usies the S3 object model and a plotting function. For details about how to use each, run help(pixelgram::pixelgram) and help(pixelgram::plot.pixelgram).

pixelgram() returns a pixelgram object for plotting.

Usage

pixelgram(tre_file = NULL, tre = NULL, nts_file = NULL, nts = NULL,
  aas_file = NULL, aas = NULL, alignment_format = "fasta", is_orf = F,
  pngs2o = F, refseq_lut = NULL, refseq_name = "HXB2",
  excise_refseq = T, master_name = "__first__", xform_master = F,
  xform_type = 0, show_tree = T, raster_width = 1,
  raster_margin = 0.025, x_lim = NULL, y_lim = NULL, invert_y = F,
  main = NULL, sub = NULL)

Arguments

tre_file	File containing Newick-formatted tree.
tre	ape phylo object in memory
nts_file	File containing nucleotide sequence alignment.
nts	seqinr nucleotide alignment in memory.
aas_file	File containing protein sequence alignment.
aas	seqinr protein alignment in memory.
alignment_format	Format of alignment file/s; must be one of these: "fasta", "clustal", "phylip", "msf", or "mase".
is_orf	flag to indicate the nt alignment is +1 codon aligned
pngs2o	Switch to mark asparagines (N) in PNG motifs as O.
refseq_lut	Look-up-table for reference numbering of alignment positions
refseq_name	Reference sequence name in the alignment. (Do not confuse "reference" sequence, used for numbering, with "master" sequence, used for coloring.)
excise_refseq	Should the reference sequence be removed from the alignment before rendering?
master_name	Name of sequence to use when showing only polymorphisms, i.e. sites that do not match. Must be a name in the alignment or one of "__first__", "__last__", "__consensus__", or "__none__". (Try not to confuse "master" and "reference" sequences. They could be the same sequence, but are used differently.)
xform_master	Should the master sequence be transformed when rendered in the pixel plot?
xform_type	Controls the way polymorphisms are shown in pixel plot; see Details.
show_tree	Show the tree? If not, only show the pixel plot.
raster_width	Proportionate width of the pixel plot, e.g. 1 indicates equal width.
raster_margin	Offset in raster portion of the layout, e.g. for heatmap.
x_lim	Range of x coordinates to use for plotting, set automatically.
y_lim	Range of y coordinates to use for plotting, set automatically.
invert_y	Should the y-axis be inverted?
main	Plot title, e.g. coded subject id. If given, it is plotted at the top of the pixelgram output.
sub	Plot subtitle, i.e. region sequenced. If specified, it appears with "site" below the pixel plot.

Details

For examples run vignette("pixelgram").

At minimum, a nucleotide sequence alignment must be provided. If no tree is given, ape::bionj will make a neighbor-joining tree with simplified parameters. The alignment can be translated (in +1 reading frame) with the standard genetic code by setting is_orf=T. For other translation options see seqinr::translate.

The refseq_name argument is used to specify standardized sequence numbering. By default it is HXB2, which will be excised from the alignment after creating a lookup-table to number positions in the alignmnent. If the exact string match to this argument is not found among sequence names in the alignment, it is searched as a regular expression, but the resulting hit is not excised from the alignment. (This is illustrated in the example vignette, in which HXB2 with a long name is not excised from the subtype reference alignment.) If excise_refseq=F the reference sequence is left in the alignment and could also become the master sequence.

The master_name argument is used when applying transformations to the pixel plot. These transformations follow the behavior of highlighter and pixel plot utilities at the LANL HIV database, i.e. only differences from the master sequence are shown in each column. The default is to use the first non-reference sequence in the alignment as the master. That is, the master sequence is set after having excised the reference sequence. In addition to names in the sequence alignment, alternative options for the master sequence include "__none__", "__first__" (the default), "__last__", and "__consensus__".

The option xform_type is an integer from 0 to 3. The default (0) means no transformation is applied, yielding a pixel plot that matches the "default" color scheme in the online pixel utility. That is, positions in all rows are colored. Other transformations will change matches to each master site as background "transparent" colors or mutational changes using an extensible color scheme. For details about how the color scheme is defined, run help(pixmap_colors). Option 3 works for amino-acid alignments to show changes in charge and potentially N-linked glycosylation sites, relative to the master sequence, but is slow to compute. Setting the option xform_master=T applies the transformation to the master sequence (following the Highlighter plot scheme, the default is F).

Value

pixelgram object

See Also

plot.pixelgram

External methods used to translate nts to aas and build a tree from nts: seqinr{translate}, ape{bionj}, and ape{dist.dna}

Online examples that are precursors to this package: http://hiv.lanl.gov/content/sequence/pixel/pixel.html and http://hiv.lanl.gov/content/sequence/HIGHLIGHT/highlighter_top.html.

Examples

## Not run: 
  plot( pg <- pixelgram::pixelgram(nts=pixelgram::hiv.ref$nts) )

## End(Not run)

phraber/pixelgram documentation built on May 25, 2019, 6:02 a.m.