make.timepoint.logos: 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

If you use the 'colors_file' option, here is an example input file (note that numbers refer to alignment slice - experimental - now refseq sites): red: 2 D magenta: blue: 2 NYO

Usage

make.timepoint.logos(x, sort_stacks = F, stacks_per_line = NULL,
  name_prefix = "logos", stratify = T, dotify = T,
  stack_width = 18, aspect_ratio = 3, show_sample_size = F,
  logo_format = "pdf", colors_file = NULL, 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.
name_prefix	String used to identify the output files.
stratify	If true, one logo plot is made per time-point sequenced.
dotify	If true, one amino-acid state per site will be left blank to indicate frequency of the TF form.
stack_width	Width of each stack, in pixels.
aspect_ratio	Adjusts aspect ratio (width to height) of image.
show_sample_size	If true, show number of sequences in the fineprint field.
logo_format	Specifies the output image format (default is 'pdf' but can also be 'png', 'svg', or 'jpeg').
colors_file	Use this option to specify different color options per site, manually. File format is as defined by ANALYZEALIGNS (see Details). Site numbers refer to (alignment slice, HXB2, alignment... TBD).
color_scheme	Defines how to color the amino acids in each site. Default is 'charge' but could also be 'monochrome', 'classic', 'hydrophobicity', or 'chemistry'). Ignored if a valid file is given for the 'colors_file' option.

Value

A vector of names of the logo plot files generated, located in a directory removed at the end of the R session. NB: You will need to copy this file (or these files) during run time or else lose them when the R session ends.

See Also

Other swarmset methods: export.fasta.swarmset, export.swarmset, plot.swarmset, print.swarmset, resample.swarmset, summary.swarmset, swarmset, tabulate.swarmset

Examples

## Not run: 
A <- lassie::swarmtools(aas_file=system.file("extdata", "CH505-gp160.fasta",
            package="lassie"), tf_loss_cutoff=80)
B <- lassie::swarmset(A)
logo.files <- make.timepoint.logos(B)
system(paste(paste("open", logo.files), collapse=';')

## End(Not run)

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