This article provides multiple solutions to create an elegant Venn diagram with R or RStudio. The following R packages will be illustrated: ggvenn, ggVenDiagram, VennDiagram and the gplots packages. Contents: Create a demo data Using the ggvenn R package Using the ggVennDiagram R package Using the VennDiagram R package Using the gplots R package Conclusion. This is a wrapper around install.packages, but with the repository chosen according to the version of Bioconductor in use, rather than to the version relevant at the time of the release of R. Install also nudges users to remain current within a release, by default checking for out-of-date packages and asking if the user would like to update.
Ggplot2 Package R
I'm using DESeq2 and Bioconductor. When loading the heatmap I got the following error message :
Here is my pipeline:
If you fail to find any function while using R just google it and see which package it comes from.
Gplots R
Sometimes you can even get their without bothering with a mouse. Though it seems this is not one of those times RSiteSearch('heatmap.2', restrict='functions') turns up another function but not the `gplots` on
Install Ggplot2 Package
I use R on both windows and a 'mainframe' linux installation (RedHat
enterprise 3.0, which they tell me is soon to be upgraded to 4.0). On
windows I installed the package gplots without trouble, and it works fine.
When I attempted to do the same on the unix computer, the following error
message was forthcoming:
downloaded 216Kb
* Installing *source* package 'gplots' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: gtools
Warning in library(pkg, character.only = TRUE, logical = TRUE, lib.loc =
lib.loc) :
there is no package called 'gtools'
Error: package 'gtools' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'gplots'
** Removing '/n/fs/disk/resuser02/u/zelickr/R/library/gplots'
The downloaded packages are in
/tmp/RtmpikM2JW/downloaded_packages
Warning messages:
1: installation of package 'gplots' had non-zero exit status in:
install.packages('gplots', lib = '~/R/library')
2: cannot create HTML package index in:
tools:::unix.packages.html(.Library)
Can someone provide the bit of information I need to progress with this?
Thanks very much,
=Randy=
R. Zelick email: [hidden email]
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Portland State University fax: 503-725-3888
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