plot.pixelgram: Renders the pixelgram object

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

Description

This layout-compatible method validates the pixelgram object, establishes plot coordinates, and draws the pixel and phylogram plots.

Usage

## S3 method for class 'pixelgram'
plot(x, xform_type = NULL, xform_master = NULL,
  leaf_colors = NULL, tip_labels = NULL, legend_attributes = NULL,
  edge_widths = NULL, edge_colors = NULL, scale_bar = NULL,
  pheno_matrix = NULL, pheno_colnames = NULL, pheno_letters = NULL,
  show_top_axis = F, show_tip_label = F, selected_rows = NULL,
  selected_row_colors = NULL, no_margin = F, plot_margin_points = F,
  vbars = NULL, raster_width = NULL, raster_margin = NULL,
  color_lut_type = NULL, x_labs = NULL, notes = NULL, annotate_env = F,
  show_tree = NULL, main = NULL, sub = NULL, ...)

Arguments

x	pixelgram object to be plotted
xform_type	see help(pixelgram::pixelgram()).
xform_master	see help(pixelgram::pixelgram()).
leaf_colors	vector of tree leaf colors; can be colors or integers
tip_labels	List for adding tree tip labels; see details.
legend_attributes	Named list of entries that go into the legend
edge_widths	tree edge widths
edge_colors	tree edge colors
scale_bar	Named list of entries used to draw the scale bar
pheno_matrix	Heatmap of RGB values to draw in raster_margin.
pheno_colnames	A vector of names to label pheno_matrix.
pheno_letters	A vector of letters to label pheno_matrix.
show_top_axis	Draw axis along top of plot?
show_tip_label	Show taxon labels on tree tips?
selected_rows	Vector of selected taxa.
selected_row_colors	Colors to depict vector of selected taxa.
no_margin	No margin? This is passed to ape::plot.phylo().
plot_margin_points	Plot margin points?
vbars	vertical bars?
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.
color_lut_type	Optional string for non-default color lookup table, currently only implemented for amino acids as 'charge' and 'taylor'.
x_labs	Vector of values to plot as labels along x axis of raster plot, e.g. to identify specific sites.
notes	Is a named list used to draw landmarks for the region sequenced, with elements "Lhs", "Rhs", "col" and "txt". Using numbering from the reference sequence lookup-table, rectangles are drawn bounded by Lhs and Rhs for each entry and filled with the color specified by col (using alpha transparency gives better results). If present, labels with values in "txt" are plotted along the margin. If annotate_env is true, these values are populated internally for the HIV-1 env.
annotate_env	If true, draw Env landmarks.
show_tree	Show the tree? If not, only show the pixel plot.
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.
...	dots, passed to ape::plot.phylo()

Details

The x-axis of the plot coordinate system is positive for the tree-plotting region, and negative for the pixel-plotting region. Setting raster_width rescales the minimum x-axis value by this factor. The default is 1, so the pixel and raster plots are equal width. The raster_margin parameter rescales the right (least negative) edge of the pixel plot, to leave a gap between pixel and tree, e.g. to include a heatmap of phyenotypic assay results.

Tree tip labels can be added by passing a list called tip_labels, with elements named "pch", "bgs", and "col". See vignette. The tree can be further decorated by passing leaf_colors, edge_widths, and edge_colors. See the last vignette example.

If defined, data in the pheno_matrix are plotted in the margin between tree and pixel plots. Entry values should be positive (non-zero) integers, which are interpreted as indices to palette(), color names, or color values. Matrix rows must have names that match tree tip-label (i.e. pg$tre$tip.label strings, or they will not be plotted. This is to facilitate their proper ordering, which follows that of the leaves on the tree. All columns are plotted, and in the order given. However, column widths are scaled to fit together into the marginal area provided within the pixel-plot area (x-values < 0) by raster_margin.

The x- and y-axis lim arguments are provided to facilitate plotting multiple trees on the same scale in different panels.

The option color_lut_type is used to specify alternative columns from the defined color scheme (see help(pixmap_colors)). For example, 'taylor' in the vignette uses the colors described in Wittgensteinean fashion by W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997).

Entries in the scale_bar list argument should be named 'pos' for plot-position coordinates, 'lwd', 'len' for bar length, in terms of the plot coordinates, 'cex', and 'text'.

Entries in the legend_attributes list argument should be named 'location' for legend positioning as defined in ?legend, 'pch', 'cex', 'pt.cex', 'lwd', 'bg', 'bty', 'box.col', 'col' for colors, 'title', and 'text'.

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.