Could not find previously saved ArchRProject in the path specified!

[susrinivasan]

Hi, I am trying to deploy Shiny ArchR and I have a directory under /srv/shiny-server/ShinyArchRUiO where all the shiny files reside. However, my ArchR project resides in my home directory /home/susrinivasan/proj_ArchR and in my global.R, I have savedArchRProject <- loadArchRProject(path="/home/susrinivasan/proj_ArchR"). I get an initialization error saying Error in loadArchRProject(path = "/home/susrinivasan/proj_ArchR") : Could not find previously saved ArchRProject in the path specified!

I am baffled as to why it says this even when my project is there and the directory is readable. I am stuck and would appreciate any help. I tried running R on the server and loading the ArchR project and it loads just fine and I could save it back. Why is the Shiny App not able to open it?

[susrinivasan]

Hi,

Thanks for your prompt response. My directory structure of ArchR project viz. projBaTP_W8_traj is as follows. @. ~]$ ls -l projBaTP_W8_traj/ total 798456 drwxr-xr-x 6 susrinivasan tnbc 4096 May 15 15:40 AMULET_multiplets_integrated drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:46 Annotations drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:39 ArrowFiles -rw-r--r-- 1 susrinivasan tnbc 126518927 Jan 5 15:17 Background-Peaks.rds drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:46 chromVar_W8_zscores drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:46 chromVar_zscores drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:46 D3to5_ATAC drwxr-xr-x 2 susrinivasan tnbc 12288 May 15 15:47 Embeddings drwxr-xr-x 4 susrinivasan tnbc 4096 May 15 15:52 GroupCoverages drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:58 ImputeWeights drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:56 IterativeLSI drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:56 IterativeLSI2 drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:56 LSI_ATAC drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:56 LSI_RNA drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:56 Monocole3 drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:57 Peak2GeneLinks drwxr-xr-x 4 susrinivasan tnbc 4096 May 15 15:57 PeakCalls drwxr-xr-x 4 susrinivasan tnbc 20480 May 15 15:58 Plots -rw-r--r-- 1 susrinivasan tnbc 23995 Jan 5 15:18 PlotsBa.adult-vs-Ba+Cycling+Ba.LP.d3to5-Down-Motifs-Enriched.csv -rw-r--r-- 1 susrinivasan tnbc 24328 Jan 5 15:18 PlotsBa.adult-vs-Ba+Cycling+Ba.LP.d3to5-Up-Motifs-Enriched.csv -rw-r--r-- 1 susrinivasan tnbc 24153 Jan 5 15:18 PlotsBa+Cycling+Ba.LP.d3to5-vs-Ba.adult-Down-Motifs-Enriched.csv -rw-r--r-- 1 susrinivasan tnbc 23978 Jan 5 15:18 PlotsBa+Cycling+Ba.LP.d3to5-vs-Ba.adult-Up-Motifs-Enriched.csv drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 15:58 Plots_integrated -rw-r--r-- 1 susrinivasan tnbc 23039 Jan 5 15:18 PlotsLP+ML+Cycling.LP.d3to5-vs-Ba+Cycling+Ba.LP.d3to5-Down-Motifs-Enriched.csv -rw-r--r-- 1 susrinivasan tnbc 24420 Jan 5 15:18 PlotsLP+ML+Cycling.LP.d3to5-vs-Ba+Cycling+Ba.LP.d3to5-Up-Motifs-Enriched.csv -rw-r--r-- 1 susrinivasan tnbc 1487 Jan 31 11:30 PlotsT1_posRegDown_Tfs.csv -rw-r--r-- 1 susrinivasan tnbc 693 Jan 31 11:30 PlotsT1_posRegUp_Tfs.csv -rw-r--r-- 1 susrinivasan tnbc 1487 Jan 31 11:40 PlotsT9_posRegDown_Tfs.csv -rw-r--r-- 1 susrinivasan tnbc 693 Jan 31 11:40 PlotsT9_posRegUp_Tfs.csv -rw-r--r-- 1 susrinivasan tnbc 736520 Jan 5 15:18 QCed_cells_snATAC_7097_1512_13012_4559_for-matching_snRNA.RData -rw-r--r-- 1 susrinivasan tnbc 690091162 May 15 16:18 Save-ArchR-Project.rds @. ~]$

I copied this entire directory projBaTP_W8_traj from my development server. If I run ShinyArchRUiO via RStudio on my development server, it is running fine. My ShinyArchRUiO on the Shiny server resides in /srv/shiny-server is in [susrinivasan@ ~]$ cd /srv/shiny-server/ [susrinivasan@ shiny-server]$ cd ShinyArchRUiO/ [susrinivasan@***** ShinyArchRUiO]$ ls -l total 4064 -rwxr-xr-x 1 susrinivasan tnbc 208 May 15 11:44 app.R -rwxr-xr-x 1 susrinivasan tnbc 142 May 15 11:44 app.R~ drwxr-xr-x 2 susrinivasan tnbc 4096 May 15 11:44 ArchRAnalysis drwxr-xr-x 2 susrinivasan tnbc 94208 May 15 11:44 ArchRLogs -rwxr-xr-x 1 susrinivasan tnbc 8480 May 16 09:13 global.R -rwxr-xr-x 1 susrinivasan tnbc 8488 May 15 16:35 global.R~ -rwxr-xr-x 1 susrinivasan tnbc 35129 May 15 11:44 LICENSE -rwxr-xr-x 1 susrinivasan tnbc 3901651 May 15 11:44 Plot-Results-W8Subtrajectory.pdf drwxr-xr-x 4 susrinivasan tnbc 4096 May 15 11:44 Plots -rwxr-xr-x 1 susrinivasan tnbc 11108 May 15 11:44 README.md -rw-r--r-- 1 susrinivasan sdsc 0 May 15 16:14 Rplots.pdf -rwxr-xr-x 1 susrinivasan tnbc 42788 May 15 11:44 server.R -rwxr-xr-x 1 susrinivasan tnbc 3251 May 15 11:44 sessionInfo_shiny_demo_instance.txt -rwxr-xr-x 1 susrinivasan tnbc 22449 May 15 11:44 ui.R

My global.r looks like

#####################################################################

Load Data

#####################################################################

Load the Saved projects folders from ArchR analysis as saved in ArchR full manual using saveArchRProject() function

Load Saved-project folders path e.g 'Save-ArchRProject2'<- loadArchRProject("path/to/your/Save-ArchRProject2"). Save project also after trajectory analysis e.g as Save-ArchRProject5

Please see ArchR full manual for saveArchRProject() function or use the ArchR.RMD for your analysis provided with the source code which follows the steps illustrated in ArchR full manual. Save-ArchRProject5

#

savedArchRProject <- loadArchRProject(path="/home/susrinivasan/projBaTP_W8_traj")

Thank you for your help.

Sumana

On Tue, May 16, 2023 at 12:08 AM Ankush Sharma @.***> wrote:

Hi @susrinivasan https://github.com/susrinivasan

ShinyArchR.UiO necessitates adhering to a folder architecture similar to that depicted in the ArchR Manual. This is because specific plots within ShinyArchR.UiO require accessing data from Arrow files in a particular manner. To facilitate your understanding, I can describe how folder paths are passed to global.R and provide an explanation of a folder architecture for analysis, although I cannot generate or provide screenshots directly. It would be helpful for better understanding of the problem , if you can share a screenshot of a folder architecture of your analysis?

Best Ankush

— Reply to this email directly, view it on GitHub https://github.com/EskelandLab/ShinyArchRUiO/issues/6#issuecomment-1549109333, or unsubscribe https://github.com/notifications/unsubscribe-auth/AV52TGDIJARLDBEUZV5VCSDXGMRYDANCNFSM6AAAAAAYC4MDZE . You are receiving this because you were mentioned.Message ID: @.***>

[ankushs0128]

ShinyArchR requires the analysis to be saved exactly as shown in ArchR Manual. If its possible, Could you please provide the input data folders as suggested in ShinyArchR.UiO readme.

Thanks

[ankushs0128]

Feel free to reopen issue, if needed more information