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netZoo / netZooR

netZooR is a network biology package implemented in R.
https://netzoo.github.io/
GNU General Public License v3.0
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Problem when compare PANDAR networks #292

Closed thangnx1012 closed 1 year ago

thangnx1012 commented 1 year ago

Discussed in https://github.com/netZoo/netZooR/discussions/291

Originally posted by **thangnx1012** August 28, 2023 Hello, I am interested in how PANDA work to create networks that fits for my study. However, I got an error when comparing data between two PANDA networks using the PandaR package, following this tutorial (https://rdrr.io/github/netZoo/netZooR/f/vignettes/pandaRApplicationinGTExData.Rmd) or even my dataset. (everything work well until) Plot the network visDiffPandaInCytoscape(diffRes_vis, condition_name = "High_Agressive", network_name="diff.PANDA") Error in visDiffPandaInCytoscape(diffRes_vis, condition_name = "High_Agressive", : could not find function "visDiffPandaInCytoscape" Apply the style to the network. Purple edges indicate higher edge weight in the defined "condition_name" parameter (HOS in our example), and green edges indicate higher edge weight in the other condition (MG63 in our example). createDiffPandaStyle(style_name="Diff.PandaStyle", condition_name="High_Agressive") Error in createDiffPandaStyle(style_name = "Diff.PandaStyle", condition_name = "High_Agressive") : could not find function "createDiffPandaStyle" I tried to copy the visDiffPandaInCytoscape function (https://rdrr.io/github/netZoo/netZooR/src/R/visDiffPandaInCytoscape.R) and createDiffPandaStyle function (https://rdrr.io/github/netZoo/netZooR/src/R/createDiffPandaStyle.R) into R, visDiffPandaInCytoscape run well so createDiffPandaStyle did not work. The console showed the message like this. Plot the network visDiffPandaInCytoscape(diffRes_vis, condition_name = "High_Agressive", network_name="diff.PANDA") You are connected to Cytoscape! Loading data... Applying default style... Applying preferred layout... networkSUID 38404 Apply the style to the network. Purple edges indicate higher edge weight in the defined "condition_name" parameter (HOS in our example), and green edges indicate higher edge weight in the other condition (MG63 in our example). createDiffPandaStyle(style_name="Diff.PandaStyle", condition_name="High_Agressive") Error in createDiffPandaStyle(style_name = "Diff.PandaStyle", condition_name = "High_Agressive") : unused arguments (style_name = "Diff.PandaStyle", condition_name = "High_Agressive") Please help me out with this issue. sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Oslo tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] devtools_2.4.5 usethis_2.2.2 tibble_3.2.1 RCy3_2.20.1 visNetwork_2.1.2 viridisLite_0.4.2 limma_3.56.2 reshape2_1.4.4 [9] ggplot2_3.4.3 fgsea_1.26.0 dplyr_1.1.2 topGO_2.52.0 SparseM_1.81 GO.db_3.17.0 AnnotationDbi_1.62.2 IRanges_2.34.1 [17] S4Vectors_0.38.1 graph_1.78.0 openxlsx_4.2.5.2 data.table_1.14.8 netZooR_1.4.0 matrixcalc_1.0-6 yarn_1.26.0 pandaR_1.32.0 [25] Biobase_2.60.0 BiocGenerics_0.46.0 reticulate_1.31 igraph_1.5.1 loaded via a namespace (and not attached):
marouenbg commented 1 year ago

adressed in discussions.