Error message with the example "The plot with the reference"

[zyb1984]

I tried to follow the example code with "The plot with the reference (https://noriakis.github.io/software/CBNplot/bngeneplot.html#the-plot-with-the-reference)", but with an error message "error in (function (classes, fdef, mtable) : The function 'convertIdentifiers' tag 'NULL' could not find inheritance methods ", also maybe with other error message "Error in UseMethod("filter") : "Filter" has no methods for "c('double', 'numeric')" target objects ", and the code
library("graphite")
library(parallel)
cl = makeCluster(4)
bngeneplot(results = pway,
exp = vsted,
expSample = incSample,
pathNum = 13, R = 30, compareRef = T,
convertSymbol = T, pathDb = "reactome",
expRow = "ENSEMBL", cl = cl)
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base

other attached packages:
[1] graphite_1.42.0 CBNplot_0.99.2
[3] DOSE_3.22.0 org.Hs.eg.db_3.15.0
[5] AnnotationDbi_1.58.0 DESeq2_1.36.0
[7] stringr_1.4.0 gridExtra_2.3
[9] tibble_3.1.7 viridis_0.6.2
[11] viridisLite_0.4.0 depmap_1.10.0
[13] ExperimentHub_2.4.0 AnnotationHub_3.4.0
[15] BiocFileCache_2.4.0 dbplyr_2.2.0
[17] dplyr_1.0.9 pheatmap_1.0.12
[19] bluster_1.6.0 scater_1.24.0
[21] ggplot2_3.3.6 scran_1.24.0
[23] scuttle_1.6.2 scRNAseq_2.10.0
[25] SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1
[27] Biobase_2.56.0 GenomicRanges_1.48.0
[29] GenomeInfoDb_1.32.2 IRanges_2.30.0
[31] S4Vectors_0.34.0 BiocGenerics_0.42.0
[33] MatrixGenerics_1.8.0 matrixStats_0.62.0

[noriakis]

Dear @zyb1984, I sincerely appreciate your detailed feedback and code.

I apologize for the error and my delayed response. Currently, the package is undergoing the reviewing process of Bioconductor and I am also updating the documentation, so some of the codes in the documentation might not work.

It seems that the code you provided works under my environment, and the error might come from environmental differences or differences in input for bngeneplot. I will look into the issue with the environment you provided, and could you please share with me the input for bngeneplot?

The comparison with the reference database can only be used with the enrichment analysis of supported pathway databases under graphite::pathways() like Reactome (pathDb="reactome") or KEGG (pathDb="kegg").
I apologize it is not currently documented and will add to the new documentation.

[noriakis]

Dear @zyb1984, Hello, thank you for your feedback. The problem seems to come from the version of reactome.db, which adds "Homo sapiens\r: " to the pathway names in the newest version. I have inserted codes to strip these prefixes in the new commit and would like to see if it works in your environment.

[wilson1990D]

Hi,Dr.noriakis, I try ro use the CBNplot with the orgDb made by myself for plant (rice), but when I entered the command as：bngeneplot(results = pwaygo,exp = gene,orgDb = osa）， but the errors as "Error in .testForValidCols(x, cols) :
Invalid columns: SYMBOL. Please use the columns method to see a listing of valid arguments.
In addition: Warning message:
In setReadable(results, OrgDb = orgDb) :
Fail to convert input geneID to SYMBOL since no SYMBOL information available in the provided OrgDb..."

[Super-dong94]

Has the problem been solved? I also appear the problem.