When trying to plot using dagLogo(t0) function,
I get an error saying:

Error in grid.Call.graphics(C_setviewport, vp, TRUE) :
non-finite location and/or size for viewport

This does not happen with the provided example data, but happens with every other data I tried. All other plotting functions (dagheatmap(t0), dagLogo(t1-t4)) work fine.

Reproducible example:

pept <- c("PSHDNEAGSVDNSEISQLLQSAATKASSLVS",
"SKPLQLKGNSENVNDSQDEEYRDDATLVKSP",
"LAAVAAASETNGKLGSEEQPEITIPKPRSSA",
"DIPVFLQIFHNFKRDSQSFLDDTVKEYTLIV",
"EAMRREMEAAMEEEISGDEEEGKTVAYLGTG",
"ESWGKQQEHQPPRKSSLETIVEKKSQAEPSG",
"EEPENNTVIEGVKEESQPDENTKEMDEVEED",
"DIPIPTSSHLLKGIDSDNDNVIREDDTGINT",
"EAVKFELSEAINNTPSLDRESERQEEEQDKE",
"DEKLTRRNELKDRSGSGTPFFETSLGREEDN")
UniProt.ws <- UniProt.ws(taxId=4932)
proteome <- prepareProteome(UniProt.ws=UniProt.ws)
#prepare dagPeptides
seq <- formatSequence(seq=pept, proteome=proteome,
upstreamOffset=15, downstreamOffset=15)
#build background model
bg <- buildBackgroundModel(seq, bg="wholeGenome", proteome=proteome)

t0 <- testDAU(seq, bg)
t1 <- testDAU(seq, bg, group="classic")
t2 <- testDAU(seq, bg, group="charge")
t3 <- testDAU(seq, bg, group="chemistry")
t4 <- testDAU(seq, bg, group="hydrophobicity")

dagHeatmap(t0)

dagLogo(t0)
dagLogo(t1, namehash=nameHash(t1@group), legend=TRUE)

Hi,

I was working with the dagLogo package for sometimes and everything worked smoothly, but suddenly I'm getting so many errors for a script that was working two months ago.

First, there was an error when I used the prepareProteome function (below)
proteome <- prepareProteome("UniProt", species = "Rattus norvegicus")
Error:

Downloading data for species: Rattus norvegicus
trying URL 'http://www.uniprot.org/uniprot/?query=organism:10116&format=fasta'
Error in download.file(url = url, destfile = tempFile, ...) :
cannot open URL 'http://www.uniprot.org/uniprot/?query=organism:10116&format=fasta'
In addition: Warning message:
In download.file(url = url, destfile = tempFile, ...) :
cannot open URL 'https://rest.uniprot.org/uniprotkb/query=organism:10116&format=fasta': HTTP status was '400 Bad Request'

---

I also tried "homo sapien" and got the same error. Anyway, I resolved this by downloading the fasta file from UniProt.

Second, which I'm still stuck with it, is for fetchSequence function:

seq <- fetchSequence(toupper(as.character(df$symbol)),
type = "uniprotswissprot",
anchorAA = as.character(df$anchor),
anchorPos = as.character(df$peptides),
proteome = proteome,
upstreamOffset=7,
downstreamOffset=7)

Error:

Error in rep(seq.int(nrow(dat)), lengths(anchorPos)) :
invalid 'times' argument

---

Here is the df table:

A tibble: 3 × 3

symbol peptides anchor

1 A0A0G2K5E8 GPKGENGIVGPTGPVGAAGPSGPNGPPGPAGSRGDGGPPGMTGfPGAAGR f
2 A0A0G2K5E8 GSDGSVGPVGPAGPIGSAGPPGfPGAPGPKGELGPVGNPGPAGPAGPR f
3 A0A0G2K5E8 GAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGfQGLPGPSGTAGEVGKPGER f

Can you help me with this? Thanks!