Guido Hooiveld

Did you also load the library `ggtangle`? [ `library(ggtangle)` ]

As said, there is indeed a known issue with resizing the nodes of an `emapplot`. This has been reported. See: https://github.com/YuLab-SMU/enrichplot/issues/308. Hopefully @GuangchuangYu is able to fix this quickly. Also:...

`enricher` performs a over-representation test. More info can be found here: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html#ora-algorithm `GeneRatio` refers to `In_category` mentioned in the example, and `BgRatio` to `not_in_category`, respectively. This expressed in the `enricher`...

Mmm, did you also try with the latest version of `clusterProfiler` (and `R`)? It is working in my hands.... ``` > get_wp_organisms() [1] "Anopheles gambiae" "Arabidopsis thaliana" [3] "Bos taurus"...

The issue is that the URL of WikiPathways has meanwhile been changed. Yet, a quick-and-dirty hack may be to source the current WikiPathways 'module' in your R-4.3.1. Doing this in...

Note that you are using an old version of `R`, and thus also of `Bioconductor`. Yet, you have installed the _current_ development version of `enrichplot` (v1.27.4.001) ... This is usually...

A pointer is given in, for example, the protocol recently published in _Nature Methods_, See section 1.9 on page 16. https://doi.org/10.1038/s41596-024-01020-z In essence you can use the `enrichKEGG` function (since...

@lungboyz When using your 13 input ids it is working for me.... For testing purposes I would set all significance cutoffs to 1 (like I do below; so that no...

Please rather use: `BiocManager::install( c('enrichplot'), force=TRUE )` `ggtangle` is available: https://cran.r-project.org/web/packages/ggtangle/index.html

@plcardozo : you indeed came up with some very useful suggestion! Hopefully @huerqiang finds some time to implement these! FYI (since you asked for hints): please note that you can...