Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

error when using "spectral" #9

Open
jamesbangbang1126 opened this issue Jun 14, 2023 · 0 comments
Open

error when using "spectral" #9

jamesbangbang1126 opened this issue Jun 14, 2023 · 0 comments

Comments

@jamesbangbang1126
Copy link

library(Spectrum)
enrichmentNetwork(enrich@result,
clustMethod = as.character("spectral"),
drawEllipses = T,
fontSize = 2.5,
repelLabels = T
)

Error in as.character(package) :
cannot coerce type 'closure' to vector of type 'character'

Thank you in advance. How to fix this problem?

R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Spectrum_1.1 plotly_4.10.1 forcats_1.0.0
[4] stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1
[7] readr_2.1.3 tidyr_1.3.0 tibble_3.1.8
[10] ggplot2_3.4.2 tidyverse_1.3.2 DOSE_3.24.2
[13] org.Hs.eg.db_3.15.0 AnnotationDbi_1.60.0 IRanges_2.32.0
[16] S4Vectors_0.36.1 Biobase_2.58.0 BiocGenerics_0.44.0
[19] clusterProfiler_4.6.0 aPEAR_1.0

loaded via a namespace (and not attached):
[1] readxl_1.4.1 shadowtext_0.1.2 backports_1.4.1
[4] fastmatch_1.1-3 plyr_1.8.8 igraph_1.3.5
[7] lazyeval_0.2.2 splines_4.2.3 gmp_0.6-10
[10] crosstalk_1.2.0 BiocParallel_1.32.5 SnowballC_0.7.0
[13] MCL_1.0 GenomeInfoDb_1.34.9 digest_0.6.31
[16] foreach_1.5.2 yulab.utils_0.0.6 htmltools_0.5.4
[19] GOSemSim_2.24.0 viridis_0.6.2 GO.db_3.15.0
[22] arules_1.7-6 fansi_1.0.4 magrittr_2.0.3
[25] memoise_2.0.1 googlesheets4_1.0.1 tzdb_0.3.0
[28] Biostrings_2.66.0 graphlayouts_0.8.4 modelr_0.1.10
[31] timechange_0.2.0 enrichplot_1.18.3 colorspace_2.1-0
[34] rvest_1.0.3 blob_1.2.3 ggrepel_0.9.3
[37] haven_2.5.1 xfun_0.37 crayon_1.5.2
[40] RCurl_1.98-1.10 jsonlite_1.8.4 scatterpie_0.1.8
[43] iterators_1.0.14 ape_5.6-2 glue_1.6.2
[46] polyclip_1.10-4 gtable_0.3.1 gargle_1.3.0
[49] zlibbioc_1.44.0 XVector_0.38.0 RcppZiggurat_0.1.6
[52] scales_1.2.1 DBI_1.1.3 Rcpp_1.0.10
[55] viridisLite_0.4.1 gridGraphics_0.5-1 tidytree_0.4.2
[58] bit_4.0.5 htmlwidgets_1.6.1 httr_1.4.4
[61] fgsea_1.24.0 RColorBrewer_1.1-3 ellipsis_0.3.2
[64] ClusterR_1.3.1 pkgconfig_2.0.3 farver_2.1.1
[67] dbplyr_2.3.0 utf8_1.2.3 labeling_0.4.2
[70] ggplotify_0.1.0 tidyselect_1.2.0 rlang_1.1.1
[73] reshape2_1.4.4 munsell_0.5.0 cellranger_1.1.0
[76] tools_4.2.3 cachem_1.0.6 downloader_0.4
[79] cli_3.6.0 generics_0.1.3 RSQLite_2.2.20
[82] gson_0.0.9 bayesbio_1.0.0 broom_1.0.3
[85] evaluate_0.20 fastmap_1.1.0 yaml_2.3.7
[88] ggtree_3.6.2 knitr_1.42 bit64_4.0.5
[91] fs_1.6.0 tidygraph_1.2.3 KEGGREST_1.38.0
[94] ggraph_2.1.0 nlme_3.1-162 aplot_0.1.9
[97] xml2_1.3.3 compiler_4.2.3 rstudioapi_0.14
[100] png_0.1-8 reprex_2.0.2 treeio_1.22.0
[103] tweenr_2.0.2 stringi_1.7.12 lattice_0.20-45
[106] Matrix_1.5-3 vctrs_0.5.2 pillar_1.8.1
[109] lifecycle_1.0.3 data.table_1.14.6 cowplot_1.1.1
[112] bitops_1.0-7 patchwork_1.1.2 qvalue_2.30.0
[115] R6_2.5.1 gridExtra_2.3 lsa_0.73.3
[118] codetools_0.2-19 MASS_7.3-58.2 assertthat_0.2.1
[121] withr_2.5.0 GenomeInfoDbData_1.2.9 diptest_0.76-0
[124] expm_0.999-7 parallel_4.2.3 hms_1.1.2
[127] grid_4.2.3 ggfun_0.0.9 HDO.db_0.99.1
[130] Rfast_2.0.7 rmarkdown_2.20 googledrive_2.0.0
[133] ggforce_0.4.1 lubridate_1.9.1

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant