Saving plotFID_live and plotVolcano_live
zillurbmb51 opened this issue · 2 comments
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
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.
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