Open jon4thin opened 10 months ago
Hi @jon4thin
The original lolliplot()
function had to be removed due to a package dependency issue. I did re-write the function which is now called Lolliplot()
as you noticed. Both function pull from biomart for protein domains. It appears however that the mirror sites for ensembl have changed without me noticing.
To fix this please try altering the host param.
object <- Lolliplot(dataset.mode1, transcript="ENST00000263967",
species="hsapiens", txdb=txdb, BSgenome=BSgenome, host="https://useast.ensembl.org")
That should resolve the issue you are having. I'll update the default host in the next release.
I was interested in using GenVisR for the lolliplot(), now Lolliplot() function.
Older versions of GenVisR have the
FField
dependency, wherebyFField
is no longer supported by bioconductor. As such, as recommended by this post by a dev of GenVisR, I got the most up to date dev version of GenVisR using the procedure on the github page:Unfortunately, now with this new GenVisR version, lolliplot() no longer functions and Lolliplot(), the replacement, is in development and non-functional. When I try the example under lolliplot() in the manual:
I get the error:
for both the mode1 and mode2 runs of Lolliplot()
Session Info: setting value version R version 4.1.2 (2021-11-01) os macOS Big Sur 10.16 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2023-11-08 rstudio 1.4.1106 Tiger Daylily (desktop) pandoc NA