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bartongroup / Proteus

R package for analysing proteomics data
MIT License
45 stars 3 forks source link

Saving plotFID_live and plotVolcano_live #39

Open zillurbmb51 opened 3 years ago

zillurbmb51 commented 3 years ago

Hello, Thank you for this excellent tool. I was trying the live images in hard disk or shiny. The plot works fine and I can see each protein one by one. When I try to save it as a html file, I can't see any proteins. Publishing in shinyapp.io (sc_up1.png and sc_up2.png) shows the following error. Any help? Best, Zillur Preparing to deploy application...DONE Uploading bundle for application: 2915488...DONE Deploying bundle: 3686361 for application: 2915488 ... Waiting for task: 799136636 building: Parsing manifest building: Pushing image: 4146884 deploying: Starting instances ################################ Begin Task Log ################################ Generating locales (this might take a while)... en_US.UTF-8... done Generation complete. [2020-09-30T08:01:23.063476463+0000] Creating dir /srv/connect/apps/iphys [2020-09-30T08:01:23.066987839+0000] Copying file meta.csv [2020-09-30T08:01:23.070195595+0000] Copying file bioinformaticianpragueexercise.zip [2020-09-30T08:01:23.074359835+0000] Creating dir /srv/connect/apps/iphys/PlotFID live _1_files [2020-09-30T08:01:23.077362119+0000] Copying file PlotFID live _1_files/html5shiv.min.js.download [2020-09-30T08:01:23.080340699+0000] Copying file proteinGroups_166_Bioinf.txt [2020-09-30T08:01:23.085556469+0000] Copying file ApicomplexanPaper.docx [2020-09-30T08:01:23.091684553+0000] Copying file bio20200057.pdf [2020-09-30T08:01:23.096426613+0000] Copying file sc_up2.PNG [2020-09-30T08:01:23.099326962+0000] Copying file sc_up1.PNG [2020-09-30T08:01:23.102547754+0000] Copying file PlotFID live _1_files/bootstrap.min.js.download [2020-09-30T08:01:23.105737832+0000] Copying file PlotFID live _1_files/bootstrap.min.css [2020-09-30T08:01:23.109165021+0000] Copying file PlotFID live _1_files/respond.min.js.download [2020-09-30T08:01:23.112402781+0000] Copying file PlotFID live _1.html [2020-09-30T08:01:23.115678945+0000] Copying file PlotFID live _1_files/shiny.css [2020-09-30T08:01:23.118700089+0000] Copying file bioinformatician_exercise.R [2020-09-30T08:01:23.121840196+0000] Copying file PlotFID live _1_files/htmlwidgets.js.download [2020-09-30T08:01:23.124951197+0000] Copying file PlotFID live _1_files/jquery.dataTables.min.js.download [2020-09-30T08:01:23.128133980+0000] Copying file PlotFID live _1_files/crosstalk.min.js.download [2020-09-30T08:01:23.131397308+0000] Copying file Bioinformatician_Position_Prague_Exercise_due_by_2020-10-01.pdf [2020-09-30T08:01:23.134782737+0000] Copying file PlotFID live _1_files/jquery.min.js.download [2020-09-30T08:01:23.137897024+0000] Copying file PlotFID live _1_files/jquery.dataTables.min.css [2020-09-30T08:01:23.140931679+0000] Copying file proteinGroups_166_Bioinf.md5 [2020-09-30T08:01:23.143888654+0000] Copying file PlotFID live _1_files/datatables.js.download [2020-09-30T08:01:23.147024055+0000] Copying file PlotFID live _1_files/json2-min.js.download [2020-09-30T08:01:23.149966202+0000] Copying file download.png [2020-09-30T08:01:23.152939682+0000] Copying file PlotFID live _1_files/datatables-crosstalk.css [2020-09-30T08:01:23.156046770+0000] Copying file PlotFID live _1_files/shiny.min.js.download [2020-09-30T08:01:23.159312123+0000] Copying file PlotFID live _1_files/jquery.dataTables.extra.css [2020-09-30T08:01:23.162406782+0000] Copying file msoutput1.txt [2020-09-30T08:01:23.167202745+0000] Copying file skype_profile.PNG [2020-09-30T08:01:23.170225661+0000] Copying file Bioinformatician_Position_Prague_data.zip [2020-09-30T08:01:23.173965165+0000] Copying file PlotFID live _1_files/crosstalk.css ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 799136673 error: Unhandled Exception: Timeout waiting for '_check_container_alive' after 0:00:30 Execution halted sc_up1 sc_up2

MarekGierlinski commented 3 years ago

Shiny interface is not the ideal for saving plots (unless you take a screenshot). I would suggest using non-live functions, plotFID or plotVolcano to create and save plots. These functions return ggplot objects, so you can use ggsave to save them in any format.

zillurbmb51 commented 3 years ago

Thank you very much. Non-live functions work fine. It would be nicer if I could save the live figures as html, because the live graphs hold all the needed information together. Best, Zillur