kerseviciute / apear Goto Github PK
View Code? Open in Web Editor NEWEnrichment Networks for Pathway Enrichment Analysis
License: MIT License
Enrichment Networks for Pathway Enrichment Analysis
License: MIT License
Thank you for providing such a good interactive plotting method to visualize the enrichment results. However, I would like to hide/remove the text on the graph nodes, how can I realize this? It seems not work when I set the fontSize=0.
Hi,
Thank you for creating such a useful package.
I have a straightforward question to ask you.
After running the function “enrichmentNetwork”, the text in the output PDF file exceeds the boundaries of the image and cannot be fully displayed. How can this issue be resolved?
I look forward to your reply.
Jeff
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
Add size and color legends.
I am using aPEAR in Rstudio, with the version aPEAR_1.0. It worked perfectly in a cloud computing env. However, in Rstudio, when I tried to use findPathClusters, I got the error telling me the function could not be found. I wonder if you could advise in this regard.
versions is as follows:
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1 IRanges_2.36.0 S4Vectors_0.40.2 Biobase_2.62.0 BiocGenerics_0.48.1 DOSE_3.28.2
[8] clusterProfiler_4.10.0 stringr_1.5.1 ggplot2_3.4.4 data.table_1.14.10 aPEAR_1.0 dplyr_1.1.4 Seurat_5.0.1
[15] SeuratObject_5.0.1 sp_2.1-2 devtools_2.4.5 usethis_2.2.2
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.2 later_1.3.2 ggplotify_0.1.2 bitops_1.0-7 tibble_3.2.1 polyclip_1.10-6
[8] fastDummies_1.7.3 lifecycle_1.0.4 globals_0.16.2 lattice_0.21-9 MASS_7.3-60 SnowballC_0.7.1 magrittr_2.0.3
[15] plotly_4.10.3 remotes_2.4.2.1 httpuv_1.6.13 sctransform_0.4.1 spam_2.10-0 sessioninfo_1.2.2 pkgbuild_1.4.3
[22] spatstat.sparse_3.0-3 reticulate_1.34.0 cowplot_1.1.2 pbapply_1.7-2 DBI_1.2.0 RColorBrewer_1.1-3 abind_1.4-5
[29] pkgload_1.3.3 zlibbioc_1.48.0 expm_0.999-8 Rtsne_0.17 purrr_1.0.2 ggraph_2.1.0 RCurl_1.98-1.13
[36] yulab.utils_0.1.2 tweenr_2.0.2 GenomeInfoDbData_1.2.11 enrichplot_1.22.0 arules_1.7-7 ggrepel_0.9.4 irlba_2.3.5.1
[43] listenv_0.9.0 spatstat.utils_3.0-4 tidytree_0.4.6 goftest_1.2-3 RSpectra_0.16-1 spatstat.random_3.2-2 fitdistrplus_1.1-11
[50] parallelly_1.36.0 leiden_0.4.3.1 codetools_0.2-19 ggforce_0.4.1 tidyselect_1.2.0 aplot_0.2.2 farver_2.1.1
[57] viridis_0.6.4 matrixStats_1.2.0 spatstat.explore_3.2-5 jsonlite_1.8.8 tidygraph_1.3.0 ellipsis_0.3.2 progressr_0.14.0
[64] ggridges_0.5.5 survival_3.5-7 iterators_1.0.14 foreach_1.5.2 tools_4.3.2 treeio_1.26.0 ica_1.0-3
[71] Rcpp_1.0.11 glue_1.6.2 gridExtra_2.3 qvalue_2.34.0 GenomeInfoDb_1.38.2 withr_2.5.2 BiocManager_1.30.22
[78] fastmap_1.1.1 fansi_1.0.6 digest_0.6.33 gridGraphics_0.5-1 R6_2.5.1 mime_0.12 colorspace_2.1-0
[85] GO.db_3.18.0 scattermore_1.2 tensor_1.5 spatstat.data_3.0-3 RSQLite_2.3.4 utf8_1.2.4 tidyr_1.3.0
[92] generics_0.1.3 graphlayouts_1.0.2 httr_1.4.7 htmlwidgets_1.6.4 scatterpie_0.2.1 uwot_0.1.16 MCL_1.0
[99] pkgconfig_2.0.3 gtable_0.3.4 blob_1.2.4 bayesbio_1.0.0 lmtest_0.9-40 XVector_0.42.0 shadowtext_0.1.2
[106] htmltools_0.5.7 fgsea_1.28.0 profvis_0.3.8 dotCall64_1.1-1 scales_1.3.0 png_0.1-8 ggfun_0.1.3
[113] rstudioapi_0.15.0 reshape2_1.4.4 nlme_3.1-163 cachem_1.0.8 zoo_1.8-12 KernSmooth_2.23-22 HDO.db_0.99.1
[120] parallel_4.3.2 miniUI_0.1.1.1 pillar_1.9.0 grid_4.3.2 vctrs_0.6.5 RANN_2.6.1 urlchecker_1.0.1
[127] lsa_0.73.3 promises_1.2.1 xtable_1.8-4 cluster_2.1.4 cli_3.6.2 compiler_4.3.2 rlang_1.1.2
[134] crayon_1.5.2 future.apply_1.11.1 plyr_1.8.9 fs_1.6.3 stringi_1.8.3 BiocParallel_1.36.0 viridisLite_0.4.2
[141] deldir_2.0-2 munsell_0.5.0 Biostrings_2.70.1 lazyeval_0.2.2 spatstat.geom_3.2-7 GOSemSim_2.28.0 Matrix_1.6-4
[148] RcppHNSW_0.5.0 patchwork_1.1.3 bit64_4.0.5 future_1.33.1 KEGGREST_1.42.0 shiny_1.8.0 ROCR_1.0-11
[155] igraph_1.6.0 memoise_2.0.1 ggtree_3.10.0 fastmatch_1.1-4 bit_4.0.5 gson_0.1.0 ape_5.7-1
For the package to be usable, license specification is required. Currently, DESCRIPTION
file contains mostly placeholder values, including:
License: What license is it under?
It would be nice to have a F/LOSS license for this package (i.e., BSD-3-Clause, MIT, LGPL-v3 just to name a few).
Return clusters assigned to each pathway
Hi,
The following error is reported while installing aPEAR:
267: edges %>%
268: .[ , xStart := lapply(from, \
^
Can it be solved?
Thanks
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