get_collectri doesn't use organism argument

[majorkazer]

The code for get_collectri (decoupleR v2.7.0) doesn't use the organism argument.

> get_collectri
function (organism = "human", split_complexes = FALSE) 
{
    collectri <- OmnipathR::collectri()
    cols <- c("source_genesymbol", "target_genesymbol", "is_stimulation", 
        "is_inhibition")

Thus, setting organism = "mouse" doesn't pull the mouse data from OmnipathR.

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] decoupleR_2.7.0    cowplot_1.1.1      openxlsx_4.2.5.1   forcats_0.5.2      stringr_1.4.1      dplyr_1.0.10       purrr_0.3.5        readr_2.1.3        tidyr_1.2.1        tibble_3.1.8       ggplot2_3.4.0     
[12] tidyverse_1.3.2    SeuratObject_4.1.3 Seurat_4.2.1      

loaded via a namespace (and not attached):
  [1] readxl_1.4.1           backports_1.4.1        plyr_1.8.8             igraph_1.3.5           lazyeval_0.2.2         sp_1.5-1               splines_4.2.0          listenv_0.8.0          scattermore_0.8       
 [10] digest_0.6.30          htmltools_0.5.3        OmnipathR_3.9.2        fansi_1.0.3            checkmate_2.1.0        magrittr_2.0.3         tensor_1.5             googlesheets4_1.0.1    cluster_2.1.3         
 [19] mixtools_2.0.0         ROCR_1.0-11            tzdb_0.3.0             globals_0.16.1         modelr_0.1.10          bayesm_3.1-5           matrixStats_0.62.0     vroom_1.6.0            timechange_0.1.1      
 [28] spatstat.sparse_3.0-0  prettyunits_1.1.1      colorspace_2.0-3       rappdirs_0.3.3         rvest_1.0.3            ggrepel_0.9.2          haven_2.5.1            xfun_0.35              crayon_1.5.2          
 [37] jsonlite_1.8.3         progressr_0.11.0       spatstat.data_3.0-0    survival_3.3-1         zoo_1.8-11             glue_1.6.2             polyclip_1.10-4        gtable_0.3.1           gargle_1.2.1          
 [46] compositions_2.0-4     leiden_0.4.3           kernlab_0.9-32         future.apply_1.10.0    BiocGenerics_0.44.0    DEoptimR_1.0-11        abind_1.4-5            scales_1.2.1           DBI_1.1.3             
 [55] spatstat.random_3.0-1  miniUI_0.1.1.1         Rcpp_1.0.9             progress_1.2.2         viridisLite_0.4.1      xtable_1.8-4           reticulate_1.26        proxy_0.4-27           bit_4.0.5             
 [64] htmlwidgets_1.5.4      httr_1.4.4             RColorBrewer_1.1-3     ellipsis_0.3.2         ica_1.0-3              pkgconfig_2.0.3        uwot_0.1.14            dbplyr_2.2.1           deldir_1.0-6          
 [73] utf8_1.2.2             tidyselect_1.2.0       rlang_1.0.6            reshape2_1.4.4         later_1.3.0            munsell_0.5.0          cellranger_1.1.0       tools_4.2.0            cli_3.4.1             
 [82] generics_0.1.3         broom_1.0.1            ggridges_0.5.4         evaluate_0.18          fastmap_1.1.0          yaml_2.3.6             goftest_1.2-3          bit64_4.0.5            knitr_1.40            
 [91] fs_1.5.2               fitdistrplus_1.1-8     zip_2.2.2              robustbase_0.95-0      RANN_2.6.1             pbapply_1.6-0          future_1.29.0          nlme_3.1-157           mime_0.12             
[100] xml2_1.3.3             compiler_4.2.0         rstudioapi_0.14        curl_4.3.3             plotly_4.10.1          png_0.1-7              e1071_1.7-13           spatstat.utils_3.0-1   viper_1.30.0          
[109] reprex_2.0.2           stringi_1.7.8          logger_0.2.2           lattice_0.20-45        Matrix_1.5-3           tensorA_0.36.2         vctrs_0.5.1            pillar_1.8.1           lifecycle_1.0.3       
[118] spatstat.geom_3.0-3    lmtest_0.9-40          RcppAnnoy_0.0.20       data.table_1.14.6      irlba_2.3.5.1          httpuv_1.6.6           patchwork_1.1.2        R6_2.5.1               promises_1.2.0.1      
[127] KernSmooth_2.23-20     gridExtra_2.3          parallelly_1.32.1      codetools_0.2-18       MASS_7.3-57            assertthat_0.2.1       withr_2.5.0            sctransform_0.3.5      parallel_4.2.0        
[136] hms_1.1.2              grid_4.2.0             class_7.3-20           rmarkdown_2.18         segmented_1.6-4        googledrive_2.0.0      Rtsne_0.16             lsr_0.5.2              spatstat.explore_3.0-5
[145] Biobase_2.58.0         shiny_1.7.3            lubridate_1.9.0    

[PauBadiaM]

Hi @majorkazer

Indeed this is a bug and we will fix it. However know that even if we solve it now, we are currently having a problem with OmnipathR and the obtained collectri network is wrong. Once we fix both problems I'll let you know. Sorry for the inconvenience.

[deeenes]

Hi @majorkazer, Now this should work, but only if you update both deceoupleR and OmnipathR from github. See details here.