User: stephen.williams

Reputation:
10
Status:
New User
Location:
Last seen:
1 year ago
Joined:
1 year, 5 months ago
Email:
s***************@10xgenomics.com

Posts by stephen.williams

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
228
views
1
answers
Comment: C: R biomaRt : listDatasets issue
... This is a known issue on Ensembl's end. I had similar issues last week and was told that they resolved the issue. Have you tried a different ensembl host? human &lt;- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl",host = "http://useast.ensembl.org/" ) Works for me ...
written 12 months ago by stephen.williams10
0
votes
0
answers
248
views
0
answers
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 13 months ago by stephen.williams10
0
votes
0
answers
248
views
0
answers
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 13 months ago by stephen.williams10
0
votes
0
answers
247
views
0
answers
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 14 months ago by stephen.williams10
0
votes
0
answers
247
views
0
answers
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 14 months ago by stephen.williams10
0
votes
1
answer
268
views
1
answers
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 15 months ago by stephen.williams10
2
votes
1
answer
268
views
1
answer
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 15 months ago by stephen.williams10 • updated 15 months ago by Robert Ivanek620
0
votes
1
answer
225
views
1
answers
Comment: C: Trouble using getBM with ecaballus_gene_ensembl
... Yes! This helps a lot. I didn't know about "external_gene_name". ...
written 15 months ago by stephen.williams10
1
vote
1
answer
225
views
1
answer
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 15 months ago by stephen.williams10 • updated 15 months ago by James W. MacDonald50k
1
vote
1
answer
522
views
1
answer
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 17 months ago by stephen.williams10 • updated 16 months ago by heir_of_isildur880

Latest awards to stephen.williams

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 217 users visited in the last hour