Getting started on the Shiny App in LatchBio | Scribe

    Getting started on the Shiny App in LatchBio

    • Jen Garbarino |
    • 15 steps |
    • 8 minutes
    information ordinal icon
    ATX R Shiny App lets you quickly explore your data in an interactive app. this tutorial walks through starting the app as well as an overview of its functions.
    1
    Click on the Pods tab
    2
    click here to start the ATX R Shiny pod. This can take up to 5 mins
    3
    If using a single shiny app pod, click the custom app button and the shiny app will open in a new tab and skip to step 9
    4
    If using multiple shiny apps or setting up a new shiny app click on RStudio
    5
    If you are adding a new shiny app into the pod go to the terminal tab and copy in the folder to the pod. To do this you can copy the path from the data tab and write the command latch cp latch://pathhere \~/ to copy into the main folder of the pod.
    6
    Go to files and click on the folder of the shiny app you would like to open
    Go to files and click on the folder of the shiny app you would like to open
    7
    Open the "server.R" file
    8
    Once open you can click "Run App" to open the shiny app in a new window.
    9
    You may need to click "Try Again" if your browser blocked the popup
    10
    Once the shiny app is open, it may take a few minutes to populate the data. Once you can see the available plots you can go through the tabs at the top for different visualizations of the data: Metadata refers to clustering and QC data (TSS, fragment counts etc) GeneAccs: Gene activity scores plotted spatially. The gene activity score refers to the overall accessibility of a gene. Can visit the following link to learn more:<https://www.archrproject.com/bookdown/calculating-gene-scores-in-archr.html> MotifEnr: Transcription factor binding motif enrichment plotted spatially Violin/Boxplot, Heatmaps and Proportion plot: visualize the data in aggregate by cluster or by sample. DE Volcano plots: view at the differential genes/motifs between samples, conditions or clusters. Motifs logo plot: the seglogo plots of the sequences for each motif Genome tracks: visualize the peaks along the genome by cluster, sample or condition The supporting tables and figures for these visualizations are available in the processed data folder
    alert ordinal icon
    If you are unable to type in additional genes from the drop, turn off the pod and then restart the app.
    information ordinal icon
    Below are a couple of tips for improving the visualization of the data for your screen and clustering
    11
    If data points are visualized too small or large on your screen "Toggle graphics controls" to change the point size
    If data points are visualized too small or large on your screen "Toggle graphics controls" to change the point size
    12
    To change the color scheme of clusters or conditions click "Toggle to subset cells" in the Metadata vs Gene Accs tab
    13
    Click on the cluster you want to change the color of. Type in the color code or use the dropdown to select a new color.
    Click on the cluster you want to change the color of. Type in the color code or use the dropdown to select a new color.
    14
    Click "KeepMyColor" to save your selections for other tabs or "DefaultColor" to return to the original clustering
    information ordinal icon
    You can also change the colors of the conditions in this tab by switching to the condition in the cell information field. Keep my color will allow this to be used in the violin/boxplot tab. You may need to click update color in this tab to refresh the plots.
    15
    When finished with visualizations, turn off the pod after closing the shiny app window.