User: zlskidmore

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zlskidmore10
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Posts by zlskidmore

<prev • 7 results • page 1 of 1 • next >
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Answer: A: how to save picture and add title to waterfall GenVisR mutation analyse?
... are you using Waterfall() or waterfall(), theres currently two function while I transition to a more object oriented style.   If you're using Waterfall() this should work:   plot <- Waterfall() pdf(file="tmp.pdf") drawPlot(plot) dev.off()     otherwise you should be able to do this:   ...
written 11 days ago by zlskidmore10
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Comment: C: Copy Number plot cnSpec - how to order samples
... This is not currently a feature in the cnSpec() function, though I think this is an oversight and more control should be given to the end user. I've created an issue for this here: https://github.com/griffithlab/GenVisR/issues/337 Not sure when I'll get around to implementing it though. ...
written 6 months ago by zlskidmore10
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Comment: C: GenVisR- cnSpec CNV plot
... cnSpec using the ggplot2 layer scale_fill_gradientn() to do colors, you might try overwriting that layer and not transition through white as it does by default. ...
written 10 months ago by zlskidmore10
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Answer: A: GenVisR- cnSpec CNV plot
... Hi Jieqiong The cnSpec function uses geom_rect() to build the plot. You can view the source code on line 86 here: https://github.com/griffithlab/GenVisR/blob/master/R/cnSpec_buildMain.R. In general I would advise against increasing the thickness of these lines as doing so would require altering the ...
written 10 months ago by zlskidmore10
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Answer: A: an error in TvTi: package GenVisR
... It looks like the maf_protein variable is storing a data.table object and not a data.frame object. I'm not sure why this would cause an issue, I suspect the issue may be the plyr package which GenVisR uses is unable to handle objects of class data.table. I'm investigating further now. Does coercing ...
written 22 months ago by zlskidmore10
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How to get the intersect and get the difference of a grange object while keeping meta data
... Hi All, I was wondering if anyone knew a way to get both the intersect and difference of a grange object while expanding out metadata columns. In other words if I had a grange object like this: gr1 <- GRanges(seqnames=c(1), ranges=IRanges(start=c(1), end=c(5)), strand=c("*"), mcols=c("a")) GRan ...
genomicranges intersect written 2.6 years ago by zlskidmore10 • updated 2.5 years ago by shepherl ♦♦ 890
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Answer: A: GenVisR Installation error message
... GenVisR also has a development page on github (see link below), you could follow the install instructions there until it is available on the Bioc-release branch. If you choose this approach it is still recommended to have R >= 3.2.2 but you won't need to download R-devel. https://github.com/grif ...
written 2.8 years ago by zlskidmore10

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