Sushi.R

[dphansti]

Hi all. Last year we released Sushi, an R package distributed by Bioconductor for the visualization of mutli-panel publication quality genomic images. Here are links to:

The paper: http://bioinformatics.oxfordjournals...ent/30/19/2808
The software (bioconductor): https://www.bioconductor.org/package...tml/Sushi.html
The software (github): https://github.com/dphansti/Sushi

Several users have asked me if there is a blog, FAQ, or forum where they can search for common questions regarding using Sushi. Please use this thread to post any questions, suggestions, or issues regarding Sushi. Thanks.

[Soumitra Ghosh]

Hi Doug, very simple (for you) first question. When I follow the Sushi documenation, with plotBedgraph I get an error message which I did not get before:

plotBedgraph(Sushi_DNaseI.bedgraph,chrom,chromstart,chromend,colorbycol= SushiColors(5))
Error: could not find function "plotBedgraph"

Thanks,
Soumitra

[blancha]

Works for me.
You'll get that error message if you haven't loaded the library.
Of course, you'll need to install the library first, or you won't be able to load it.

source("http://bioconductor.org/biocLite.R")
biocLite("Sushi")

library(Sushi)

data(Sushi_ChIPSeq_CTCF.bedgraph)
data(Sushi_DNaseI.bedgraph)

chrom            = "chr11"
chromstart       = 1955000
chromend         = 1965000
plotBedgraph(Sushi_DNaseI.bedgraph,chrom,chromstart,chromend,colorbycol= SushiColors(5))

[Soumitra Ghosh]

I appreciate your help, but I did try that before I asked the question on this forum. I wonder if there is any other explanation?

[blancha]

Post the output of the following command.

sessionInfo()

[Soumitra Ghosh]

Did what you suggested. Got the same message so a systematic issue here...what is your suggestion:
> sessioninfo()
Error: could not find function "sessioninfo"

[GenoMax]

See the capital "I" in sessionInfo that @blancha requested.

[Soumitra Ghosh]

Sorry, with the right command i get:

> sessionInfo
function (package = NULL) 
{
    z <- list()
    z$R.version <- R.Version()
    z$platform <- z$R.version$platform
    if (nzchar(.Platform$r_arch)) 
        z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
    z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer, 
        "-bit)")
    z$locale <- Sys.getlocale()
    if (is.null(package)) {
        package <- grep("^package:", search(), value = TRUE)
        keep <- sapply(package, function(x) x == "package:base" || 
            !is.null(attr(as.environment(x), "path")))
        package <- sub("^package:", "", package[keep])
    }
    pkgDesc <- lapply(package, packageDescription, encoding = NA)
    if (length(package) == 0) 
        stop("no valid packages were specified")
    basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && 
        x$Priority == "base")
    z$basePkgs <- package[basePkgs]
    if (any(!basePkgs)) {
        z$otherPkgs <- pkgDesc[!basePkgs]
        names(z$otherPkgs) <- package[!basePkgs]
    }
    loadedOnly <- loadedNamespaces()
    loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
    if (length(loadedOnly)) {
        names(loadedOnly) <- loadedOnly
        pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
        z$loadedOnly <- pkgDesc[loadedOnly]
    }
    class(z) <- "sessionInfo"
    z
}
<bytecode: 0x0000000008e96130>
<environment: namespace:utils>
>

[dphansti]

Make sure you add the parentheses. You executed this:

sessionInfo

You need to execute this:

sessionInfo()

[blancha]

When you call a function in R, you need to add the parentheses at the end of the call to the function.

sessionInfo()

Otherwise, you'll just get the code for the function, as you just did.

I really think you just haven't loaded the package.
It would lead to exactly the error message you are getting.
The package works fine.
With the package loaded, I am unable to reproduce your error message despite several attempts (older versions of the package, different computers, ...).

When you type sessionInfo(), you must see Sushi in your list of attached packages, before making the call to plotBedgraph.
If Sushi is not in the output after you type sessionInfo(), you have discovered the problem.
If it is in the path, which I doubt, your problem is more complex, and will require further troubleshooting.
The output of sessionInfo() will still be useful to the package developer, if there is really a bug in the code and not a user error.

[Soumitra Ghosh]

Thank you blancha, makes sense. I did have Sushi running well before and when I came back after a few weeks I got the above error message. Will try and reload. Appreciate your help.

[JPreston]

Formatting Axes with plotBedgraph

Hi,

I am using plotBedgraph to a figure that plots SNP allele frequencies across a genome with two separate tracks, using the example in the Sushi vignette. It almost works perfectly but I am wishing that the y axis on the two tracks were the same (both from 0-0.2). Is there a way to change the scale of the axes?

It also would be nice if the red track was on the top but when I switch those I can't also get the colors on the legend to switch so that red is on top. I have been trying everything I've seen on here so far and am still unable to get this to work. I really appreciate any help.

Here is my code:

par(mfrow=c(2,1),mar=c(1,4,1,1))
plotBedgraph(bottle,chrom,chromstart,chromend,transparency=.50,
color=SushiColors(2)(2)[1])
axis(side=2, las=2,tcl=.2)
mtext("Allele Freq",side=2,line=3,cex=1,font=1)
legend("topright",inset=0.025,legend=c("Lab-only SNPs","Wild-only SNPs"),
fill=opaque(SushiColors(2)(2)),border=SushiColors(2)(2),text.font=2,
cex=1.0)
plotBedgraph(denovo, chrom, chromstart, chromend,
transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])
labelgenome(chrom,chromstart,chromend,side=3,n=2,scale="Kb")
axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),
labels=-1*pretty(par("yaxp")[c(1,2)]))
mtext("Allele Freq",side=2,line=3,cex=1,font=1)

[dphansti]

Sure. This shouldn't be too hard.

In order to set the y axis to a specific value just add the argument ymax=0.2 when you call plotBedgraph.

In order to switch the colors it is probably easiest just to set the colors manually rather than using SushiColors. Try running the code below (I have not tested it since I don't have your data but I think it should work). Good luck!


par(mfrow=c(2,1),mar=c(1,4,1,1))
plotBedgraph(bottle,chrom,chromstart,chromend,transparency=.50,
color="firebrick2",ymax=0.2)
axis(side=2, las=2,tcl=.2)
mtext("Allele Freq",side=2,line=3,cex=1,font=1)
legend("topright",inset=0.025,legend=c("Lab-only SNPs","Wild-only SNPs"),
fill=opaque(c("firebrick2","dodgerblue2")),border=c("firebrick2","dodgerblue2"),text.font=2,
cex=1.0)
plotBedgraph(denovo, chrom, chromstart, chromend,
transparency=.50, flip=TRUE, color="dodgerblue2",ymax=0.2)
labelgenome(chrom,chromstart,chromend,side=3,n=2,scale="Kb")
axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),
labels=-1*pretty(par("yaxp")[c(1,2)]))
mtext("Allele Freq",side=2,line=3,cex=1,font=1)

[JPreston]

Awesome thanks!!! The axes got weird when I tried to flip them, but it works fine if they are parallel. The colors work great too!