Closed YunielFM closed 2 years ago
Hey @YunielFM,
Thanks for using the package and your kind words!
The terms are by default ranked by lowest_p
(in increasing order), this is used by enrichment_chart()
in the wrapper to plot the top 10 terms.
For each iteration (by default 10) of run_pathfindR()
, active subnetwork search yields 100s of subnetworks (each of these are then used for enrichment analyses). support
is the median proportion of active subnetworks leading to enrichment within an iteration over all iterations. Thus, a higher support would indicate a pathway/term that is supported by a larger proportion of subnetworks.
Hope this helps, Best, -E
Hi Ege, first of all, CONGRATS on this fantastic package! I have been using it even before you officially placed it on the CRAN! I have gone through the most recent documentation (again, great stuff!) but I am missing the relationship between the default top10 items used in the
enrichment_chart
and the actual information calculated with the wrapperrun_pathfindR
. Which are the criteria for those top10 terms? It does not seem to correspond to any ranked values from the columnsFold_Enrichment
,occurrence
,support
,lowest_p
, orhighest_p
. Additionally, I fail to see a description of what thesupport
metric refers to.Default output when visualizing the
Which matches the default order of the ![image](https://user-images.githubusercontent.com/51164590/153762028-c1c7ee9a-4e2b-47a7-9f7e-fadacdc349b5.png)
enrichment_chart
result:run_pathfindR
result:As you can see, these terms are not top-ranked by any metric, hence it would be great to correct it for users that do not go under the hood to extract the data.
Desktop (please complete the following information): Windows 10 x64 (build 22000)
R Session Information: R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods base
other attached packages: [1] BiocStyle_2.20.2 org.Hs.eg.db_3.13.0 AnnotationDbi_1.54.1 IRanges_2.26.0 S4Vectors_0.30.0 Biobase_2.52.0
[7] BiocGenerics_0.38.0 ggVennDiagram_1.2.0 pathfindR_1.6.3 pathfindR.data_1.1.2 conflicted_1.1.0 kableExtra_1.3.4
[13] KEGGREST_1.32.0 KEGGgraph_1.52.0 readxl_1.3.1 ggpubr_0.4.0 RColorBrewer_1.1-2 cowplot_1.1.1
[19] wesanderson_0.3.6 ggsci_2.9 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8 readr_2.1.2
[25] tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 ComplexHeatmap_2.8.0 purrr_0.3.4
[31] biomaRt_2.48.3
loaded via a namespace (and not attached): [1] backports_1.4.1 circlize_0.4.14 BiocFileCache_2.0.0 systemfonts_1.0.4 igraph_1.2.11 lazyeval_0.2.2
[7] crosstalk_1.2.0 GenomeInfoDb_1.28.4 digest_0.6.29 foreach_1.5.2 htmltools_0.5.2 magick_2.7.3
[13] viridis_0.6.2 fansi_1.0.2 magrittr_2.0.1 memoise_2.0.1 cluster_2.1.2 doParallel_1.0.17
[19] tzdb_0.2.0 graphlayouts_0.8.0 Biostrings_2.60.2 modelr_0.1.8 matrixStats_0.61.0 vroom_1.5.7
[25] svglite_2.1.0 prettyunits_1.1.1 RVenn_1.1.0 colorspace_2.0-2 ggrepel_0.9.1 blob_1.2.2
[31] rvest_1.0.2 rappdirs_0.3.3 haven_2.4.3 xfun_0.29 crayon_1.4.2 RCurl_1.98-1.6
[37] jsonlite_1.7.3 graph_1.70.0 iterators_1.0.14 glue_1.6.1 polyclip_1.10-0 gtable_0.3.0
[43] zlibbioc_1.38.0 XVector_0.32.0 webshot_0.5.2 GetoptLong_1.0.5 car_3.0-12 Rgraphviz_2.36.0
[49] shape_1.4.6 abind_1.4-5 scales_1.1.1 DBI_1.1.2 rstatix_0.7.0 Rcpp_1.0.8
[55] viridisLite_0.4.0 progress_1.2.2 units_0.8-0 clue_0.3-60 proxy_0.4-26 bit_4.0.4
[61] DT_0.20 htmlwidgets_1.5.4 httr_1.4.2 ellipsis_0.3.2 farver_2.1.0 pkgconfig_2.0.3
[67] XML_3.99-0.8 sass_0.4.0 dbplyr_2.1.1 utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.1
[73] rlang_1.0.1 munsell_0.5.0 cellranger_1.1.0 tools_4.1.2 cachem_1.0.6 cli_3.1.1
[79] generics_0.1.2 RSQLite_2.2.9 broom_0.7.12 evaluate_0.14 fastmap_1.1.0 yaml_2.2.2
[85] knitr_1.37 bit64_4.0.5 fs_1.5.2 tidygraph_1.2.0 ggraph_2.0.5 xml2_1.3.3
[91] compiler_4.1.2 rstudioapi_0.13 plotly_4.10.0 filelock_1.0.2 curl_4.3.2 png_0.1-7
[97] e1071_1.7-9 ggsignif_0.6.3 reprex_2.0.1 tweenr_1.0.2 bslib_0.3.1 stringi_1.7.5
[103] highr_0.9 classInt_0.4-3 vctrs_0.3.8 pillar_1.7.0 lifecycle_1.0.1 BiocManager_1.30.16
[109] jquerylib_0.1.4 GlobalOptions_0.1.2 data.table_1.14.2 bitops_1.0-7 R6_2.5.1 KernSmooth_2.23-20
[115] gridExtra_2.3 codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1 rjson_0.2.21 withr_2.4.3
[121] GenomeInfoDbData_1.2.6 hms_1.1.1 class_7.3-19 rmarkdown_2.11 carData_3.0-5 Cairo_1.5-14
[127] sf_1.0-6 ggforce_0.3.3 lubridate_1.8.0