plot.swarmset: Render a logo plot of concatamer forms of clones in...

In phraber/lassie: Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

Description

Render a logo plot of concatamer forms of clones in working_swarm

Usage

## S3 method for class 'swarmset'
plot(x, sort_stacks = F, stacks_per_line = NULL,
  dotify = F, color_scheme = "charge", ...)

Arguments

x	A swarmset object populated with working_swarm.
sort_stacks	If true, reorder sites from left to right.
stacks_per_line	If NULL, this is set to the number of selected sites; otherwise, it limits plot width.
dotify	If true, one amino-acid state per site will be left blank to indicate frequency of the TF form.
color_scheme	Defines how to color the amino acids in each site. Default is 'charge' but could also be 'monochrome', 'classic', 'hydrophobicity', or 'chemistry').
...	can include "aspect_ratio" to adjust Aspect ratio (width to height) of image and "format" to specify the output image format (default is 'png_print' (600dpi resolution) but can also be 'png' (96dpi), 'pdf', 'svg', or 'jpeg').

Value

An explicit path to the file generated, located in a directory removed at the end of the R session. NB: You will need to copy this file during run time or else lose it when the R session ends.

See Also

Other swarmset methods: export.fasta.swarmset, export.swarmset, make.timepoint.logos, print.swarmset, resample.swarmset, summary.swarmset, swarmset, tabulate.swarmset

phraber/lassie documentation built on May 25, 2019, 6:01 a.m.