plotDNA: Plot a bunch of DNA sequences

In sherrillmix/dnaplotr: Plot a Collection of DNA Sequences

Plot a bunch of DNA sequences

Description

Take a vector of strings representing DNA sequences and plot them to the current device. A, C, T and G are colored, - are colored gray and all other characters are white.

Usage

plotDNA(
  seqs,
  seqCounts = rep(1, length(seqs)),
  cols = c(A = "green", T = "red", C = "blue", G = "yellow", `-` = "grey", default =
    "white"),
  xlab = "Position",
  ylab = "Sequence Read",
  display = c(groups = !is.null(groups)),
  xStart = 1,
  groups = NULL,
  groupCexScale = FALSE,
  refSeq = NULL,
  res = 0,
  ...
)

plotAA(..., mar = NULL, cols = dnaplotr::aminoCols)

Arguments

seqs	A character vector containing DNA sequences
seqCounts	A integer vector with the number of counts for each sequence. This can be used to improve run time and file size if some sequences are duplicated multiple times (default: 1 for each entry in seqs)
cols	A named vector with names corresponding to the DNA bases and values showing the appropriate color (default: A: green, T: red, C: blue, G: yellow, -: grey)
xlab	A string specifying the x-axis label (default: Position)
ylab	A string specifying the y-axis label (default: Sequence read)
display	A logical vector with element names in 'legend', 'xAxis', 'yAxis', 'groups' where a FALSE suppresses outputting that plot element (default: TRUE for all or any missing elements)
xStart	First base in plot should be labelled as this (default: 1)
groups	Group sequences by group and show label on right side of plot. Note that any prior ordering of sequences will be disrupted. Use a factor and reorder the levels to set a particular order of groups.
groupCexScale	A logical whether to scale group label size by the number of sequences. Useful to highlight more abundant groups and help squeeze in labels on smaller groups.
refSeq	Reference sequence used for numbering the x-axis without counting gaps present in this sequence (note that for further annotations outside this function, e.g. abline(v=3), the axis will be from xStart:xStart+max(nchar(seqs)) without any adjustments to ignore reference gaps
res	If res greater than 0 then render the colors as a raster graphic with this res x res resolution. Useful for embedding a raster graphic inside a pdf where the file size would otherwise be too large. Note that this parameter is best left at 0 except in special circumstances.
...	Additional arguments to plot
mar	margin sizes as in par. If left at default then use the current margin settings increasing margin[1] (bottom) to 6.5 if less than 6.5 (needed to give the amino acid legend more space by default). Set explicitly if this behavior is undesired.

Value

an invisible vector of the mean vertical position for groupings (empty if 'groups' is null)

Functions

• plotAA(): Plot a bunch of AA sequences

Examples

plotDNA(c('ACACA','ACACA','ACACT'))
refSeq<-'AC---A'
seqs<-c('ACTGGA','ACTGCA','ACTGGC','GCTGGG','GGGG',refSeq)
par(mar=c(4,5,.5,6),cex.axis=2,cex.lab=2)
groupOrder<-c('Group2','Group1','Group3','Reference')
groups<-factor(c('Group1','Group2','Group3','Group1','Group3','Reference'),levels=groupOrder)
seqCounts<-c(30,10,10,15,5,5)
plotDNA(seqs,seqCounts=seqCounts,groups=groups,xStart=10,groupCexScale=TRUE,refSeq=refSeq)
fakeSeqs<-createFakeDNA(1000)
refSeq<-fakeSeqs[1]
fakeSeqs<-fakeSeqs[-1]
species<-sprintf('Species %s',sub(' [0-9]+$','',names(fakeSeqs)))
par(mar=c(3.5,4.4,.5,7))
plotDNA(fakeSeqs,groups=species,groupCexScale=TRUE)
fakeAA<-c('MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALY',
'MALWTRLRPLLALLALWPLPPARAFVNQHLCGSHLVEALY',
'MALWTRLRPLLALLALWPPPPARAFVNX')
plotAA(fakeAA,groups=c('Ref','Sub','Stop'))
#set res>0 if vector file sizes are too large
plotAA(fakeAA,groups=c('Ref','Sub','Stop'),res=500)

sherrillmix/dnaplotr documentation built on Oct. 29, 2022, 4:42 p.m.