Errors working through the Functional annotation vignette

[kylepalos]

Hi,

Thanks for creating a really nice plant-focused package. I am working with Maize scRNA data in the Pre-processing and Functional annotation vignettes as follows:

library(scPlant)
library(CellFunTopic)

early1 <- readData(data="outs/filtered_feature_bc_matrix",
         type = "10X",
         species = "Zea mays")

early1 <- QCfun(early1)
early1 <- RunSeurat(early1, resolution = 1.5)

early1 <- RunGSEA_plant(early1, by = 'GO', release_version = "Zm-B73-REFERENCE-NAM-5.0", minpct = .25)

The above code all completed successfully, and I can find the various objects generated in the

early1@misc

slots

However, when trying to proceed in the functional annotation vignette, I get errors with all of the following functions:

pathway_unique_shared(early1, by = "GO", fontsize_row = 5, 
                      toshow = "-logFDR")

Error in UseMethod("mutate") : 
  no applicable method for 'mutate' applied to an object of class "NULL"

hierarchyplot_tree(early1, by = "GO", topaths = 4, cluster_cutree_k = 14, pathway_cutree_k = 14,
                   vertex.label.cex=0.5, edge.max.width=1, vertex.size.cex=0.7)

Error in UseMethod("filter") : 
  no applicable method for 'filter' applied to an object of class "NULL"

early1 <- runLDA(early1, k = 23)

Error in UseMethod("mutate") : 
  no applicable method for 'mutate' applied to an object of class "NULL"

These seem to be Dplyr errors based on not having a valid data frame object to work on. Am I doing something incorrect?

Thank you very much for your help.

[xiaobaicainiao666]

Sorry for the late reply. The source code for the function RunGSEA_plant has been modified to rectify these errors. If you prefer not to reinstall the scPlant package, consider the following alternative: early1@misc$GSEAresult_GO <- early1@misc$GSEAresult_customized Running the code above before proceeding to the functional annotation vignette may help to avoid these errors.