could not find function "plot_enrichment"

[FernandoTobias]

Hi,

I'm having trouble obtaining the desired output for an enrichment analysis. I did the following:

de_results <- de_analysis(d, Core - Monolayer) Warning message: Zero sample variances detected, have been offset away from zero enrich_results = lsea(de_results) Warning messages: 1: In fgsea::fgsea(pathways = pathways, stats = stats, minSize = minSize, : You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call. 2: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.73% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results. 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading 7: In serialize(data, node$con) : 'package:stats' may not be available when loading 8: In serialize(data, node$con) : 'package:stats' may not be available when loading significant_lipidsets(enrich_results) $Core - Monolayer [1] "Class_LPI" "total_cs_0" "Class_HexCer"

plot_enrichment(de_results, significant_lipidsets(enrich_results), annotation="class") Error in plot_enrichment(de_results, significant_lipidsets(enrich_results), : could not find function "plot_enrichment"

Thanks, Fernando Tobias

[ahmohamed]

Can you check which lipidr version is installed. plot_enrichment(annotation="class") was added in version 2.4 to replace plot_class_enrichment. If you're using older version, please update or use plot_class_enrichment.

[FernandoTobias]

Just updated to 2.4. It works now! Thanks.