User: stephen.williams

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Posts by stephen.williams

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Gviz: Histograms in layers instead of stacked
... Once again, I have figured out my own question. The OverlayTrack function is the solution. Thanks to bioconductor support for being a great sounding board! ...
written 18 days ago by stephen.williams10
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Gviz: Histograms in layers instead of stacked ANSWERED!
... I am plotting a set of data that I'd like to layer on top of each other. This is sequencing read depth from two samples. Here a snippet of my data GRanges object with 3828 ranges and 2 metadata columns: seqnames ranges strand | depth1 depth2 <Rle> ...
gviz R gviz-package written 19 days ago by stephen.williams10
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Comment: C: Gviz: Multiple BiomartGeneRegionTrack one object for Composite plots
... For anyone interested I got this to work by ultimately plotting my tracks as per below. This method should be able to take any number of tracks and combine as many loci as you'd like. grid.newpage() pushViewport(viewport(layout = grid.layout(2,1))) pushViewport(viewport(layout.pos.col = ((1 -1)%% ...
written 4 weeks ago by stephen.williams10
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Gviz: Multiple BiomartGeneRegionTrack one object for Composite plots
... I'm trying to make a Composite plot of multiple gene regions. I've read the vignette, Chapter 6 on doing this. I'm able to plot my data but not the GeneRegionTrack using. chroms <- c("chr2", "chr17") ncols <- 1 nrows <- length(chroms)%/%ncols grid.newpage() pushViewport(view ...
gviz gviz-package written 4 weeks ago by stephen.williams10
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Comment: C: Gviz: Flip tracks so 5 prime end always on left hand side.
... Hi Robert, Thanks for the very helpful, albeit very snarky, response. I have spent hours with this vignette but did not remember this section. For anyone who is interested these display parameters can be found in the settings {Gviz} section of the R documentation ...
written 8 weeks ago by stephen.williams10
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Gviz: Flip tracks so 5 prime end always on left hand side.
... I'm plotting a BiomartGeneRegionTrack() and some DataTrack() using Gviz for a bunch of genes. This is going fine and the plots look great. I it would be really nice to have all the 5' ends of the genes of interest begin on the left hand side of the track. Is there a way to simply "flip" this track ( ...
gviz gviz-package written 8 weeks ago by stephen.williams10 • updated 8 weeks ago by Robert Ivanek530
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Comment: C: Trouble using getBM with ecaballus_gene_ensembl
... Yes! This helps a lot. I didn't know about "external_gene_name". ...
written 9 weeks ago by stephen.williams10
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Trouble using getBM with ecaballus_gene_ensembl
... I'm having trouble querying biomart using the biomaRt package for a non human species. for example, this works library('biomaRt') mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") getBM(attributes = c('entrezgene','hgnc_symbol', 'ensembl_gene_id'), filters = 'hgnc_symbol', ...
biomart biomartr written 9 weeks ago by stephen.williams10 • updated 9 weeks ago by James W. MacDonald46k
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Font size plotGOgraph
... I'm plotting the output of enrichGO from the clusterProfiler package. The font size is so small it is illegible (even in the Vignette here: https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf).  Is there a way to increase the font and node size?   Many thanks,   St ...
clusterprofiler plotgograph written 3 months ago by stephen.williams10 • updated 3 months ago by heir_of_isildur880
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Comment: C: Gviz: Draw horizontal line on DataTrack
... Hi Robert, Yes, I have pored over this vignette many times. The problem is that I want to plot mean and sd across loci whereas the Data Grouping section provides mean and ci within loci. I only have one group as well. For example if I have 4 data points at a given region, 1,3,5,7 I'd like to plot l ...
written 4 months ago by stephen.williams10

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