Development protocol of Digital Sorter

Main structure

• ui.R User interface. Use shinydashboard.

• server.R Where the main codes are.

• global.R Library all the needed packages.

• R/ util.R

  All the .R files in the R/ folder would be read/sourced automatically by the shiny app. The functions used in the app could be placed in the .R file. Currently, this file includes three functions:

  • get_cell_markers: Get cell surface protein via MSigDB GOCC_CELL_SURFACE set.

    Union.cell.surface.marker <- get_cell_markers(category = "C5",
                                                  subcategory = "GO:CC",
                                                  set_name = "GOCC_CELL_SURFACE")
    

  • ReadRDSFiles: Automatically read all the .rds files in /data folder. (only once when the docker is launched)
  • getMarkers: Marker selection function. modified from cerebroApp getMarkerGenes.R.

• www/

  All the images in the www/ folder could be sourced by the shiny app with the code img(src = "file_name.PNG", width=550, height=480).

• data/

  All the rds file in the data/ folder would be read by ReadRDSFiles function. Please do not change the names of the following files!!

  • Union.cell.surface.marker.rds: a character string of cell surface markers

  • datasets.rds: should be a **SplitObject ** of seurat. SplitObject(ob, split.by = "dataset_origin")

  • markerlist.rds: should be a list including master markers of interested cancer types.

    

Event reactive objects

The reactive seurat objects in different panels are all independent.

After users select the cohort (dataset), the reactive seurat objects are named ob_reactive_h (for violin plots), ob_reactive1 (for dot plots in gene of interest panel), ob_reactive2 (for dot plots in marker selection panel) in the server.R.

After users select the disease type, the reactive seurat objects are named ob_selected1 (for dot plots in gene of interest panel), ob_selected2 (for dot plots in marker selection panel) in the server.R.