Error in UseMethod("rescale")
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vvelagal • 0
@2528ae94
Last seen 7 weeks ago
United States

While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package

gse <- enrichGO(gene = deGenes, ont = "BP",
                   OrgDb ="org.Dm.eg.db",
                   universe = geneUniverse,
                   readable=TRUE,
                   pvalueCutoff = 0.05)

 cnetplot(gse, categorySize="pvalue", foldChange=gene_list, showCategory =20, font.size=12,label_format=30,cex_line =1,colorEdge = TRUE)

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

Session info ()

Matrix products: default



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

other attached packages:
 [1] DOSE_3.20.1           enrichplot_1.14.2     clusterProfiler_4.2.2 org.Dm.eg.db_3.14.0   AnnotationDbi_1.56.2 
 [6] IRanges_2.28.0        S4Vectors_0.32.4      Biobase_2.54.0        BiocGenerics_0.40.0   reshape2_1.4.4       
[11] MASS_7.3-58.1         ggplot2_3.4.0         gplots_3.1.3         

loaded via a namespace (and not attached):
  [1] fgsea_1.20.0           ggnewscale_0.4.8       colorspace_2.0-3       ggtree_3.2.1           qvalue_2.26.0         
  [6] XVector_0.34.0         aplot_0.1.8            rstudioapi_0.14        farver_2.1.1           graphlayouts_0.8.3    
 [11] ggrepel_0.9.2          bit64_4.0.5            fansi_1.0.3            scatterpie_0.1.8       splines_4.1.2         
 [16] cachem_1.0.6           GOSemSim_2.20.0        polyclip_1.10-4        jsonlite_1.8.3         broom_1.0.1           
 [21] GO.db_3.14.0           png_0.1-7              ggforce_0.4.1          compiler_4.1.2         httr_1.4.4            
 [26] backports_1.4.1        assertthat_0.2.1       Matrix_1.4-0           fastmap_1.1.0          lazyeval_0.2.2        
 [31] cli_3.1.1              tweenr_2.0.2           tools_4.1.2            igraph_1.3.5           gtable_0.3.1          
 [36] glue_1.6.2             GenomeInfoDbData_1.2.7 DO.db_2.9              dplyr_1.0.10           fastmatch_1.1-3       
 [41] Rcpp_1.0.9             vctrs_0.5.0            Biostrings_2.62.0      ape_5.6-2              nlme_3.1-155          
 [46] ggraph_2.1.0           stringr_1.4.1          lifecycle_1.0.3        gtools_3.9.3           zlibbioc_1.40.0       
 [51] scales_1.2.1           tidygraph_1.2.2        parallel_4.1.2         RColorBrewer_1.1-3     memoise_2.0.1         
 [56] gridExtra_2.3          downloader_0.4         ggfun_0.0.8            yulab.utils_0.0.5      stringi_1.7.6         
 [61] RSQLite_2.2.18         tidytree_0.4.1         caTools_1.18.2         BiocParallel_1.28.3    GenomeInfoDb_1.30.1   
 [66] rlang_1.0.6            pkgconfig_2.0.3        bitops_1.0-7           lattice_0.20-45        purrr_0.3.5           
 [71] treeio_1.18.1          patchwork_1.1.2        labeling_0.4.2         shadowtext_0.1.2       bit_4.0.4             
 [76] tidyselect_1.2.0       plyr_1.8.7             magrittr_2.0.3         R6_2.5.1               snow_0.4-4            
 [81] generics_0.1.3         DBI_1.1.3              pillar_1.8.1           withr_2.5.0            KEGGREST_1.34.0       
 [86] RCurl_1.98-1.9         tibble_3.1.8           crayon_1.5.2           KernSmooth_2.23-20     utf8_1.2.2            
 [91] viridis_0.6.2          grid_4.1.2             data.table_1.14.4      blob_1.2.3             digest_0.6.30         
 [96] tidyr_1.2.1            gridGraphics_0.5-1     munsell_0.5.0          viridisLite_0.4.1      ggplotify_0.1.0    
clusterProfiler • 645 views
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You need to check that enrichGO correctly worked, otherwise there may be an issue in creating your data. Look closely at each step of your code and the resulting objects

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Entering edit mode

To add to Basti's comment: you may also need to update, since it is working in my hands using the latest version of R/Bioconductor.

> library(clusterProfiler)
> 
> ## use sample data
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01, readable=TRUE)

> 
> ## create cnetpplot. It is working fine.
> ## notice the deprecation warning when generating the cnetplot
> cnetplot(yy, categorySize="pvalue", foldChange=geneList, showCategory=20, font.size=12, label_format=30, cex_line =1, colorEdge = TRUE)
Scale for size is already present.
Adding another scale for size, which will replace the existing scale.
Warning messages:
1: In cnetplot.enrichResult(x, ...) :
  Use 'color.params = list(foldChange = your_value)' instead of 'foldChange'.
 The foldChange parameter will be removed in the next version.
2: In cnetplot.enrichResult(x, ...) :
  Use 'color.params = list(edge = your_value)' instead of 'colorEdge'.
 The colorEdge parameter will be removed in the next version.
3: ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
> 
> ## this will be the new way of providing the arguments.
> color.params = list(foldChange = geneList, edge = TRUE)
> cnetplot(yy, color.params = color.params, categorySize="pvalue", showCategory =20, font.size=12, label_format=30, cex_line =1)
Scale for size is already present.
Adding another scale for size, which will replace the existing scale.
Warning message:
ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
> 
>
> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
[1] clusterProfiler_4.6.0

loaded via a namespace (and not attached):
  [1] nlme_3.1-160           bitops_1.0-7           ggtree_3.6.2          
  [4] enrichplot_1.18.1      bit64_4.0.5            HDO.db_0.99.1         
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