An interactive web portal for exploring immuno-oncology data
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README.md

Shiny-iAtlas

Shiny-iAtlas is an interactive web portal that provides multiple analysis modules to visualize and explore immune response characterizations across cancer types. The app is hosted on shinyapps.io at https://isb-cgc.shinyapps.io/shiny-iatlas/ and can also be accessed via the main CRI iAtlas page at http://www.cri-iatlas.org/.

The portal is built entirely in R and Shiny using the RStudio development environment. Layout and interactivity within the portal are achieved by heavy use of the following packages:

  • shinydashboard
  • plotly
  • crosstalk

Violin plots are not available in the current version of plotly in CRAN; need to use development version from GitHub (e.g., 4.7.1.9000). To install the development version:

devtools::install_github("ropensci/plotly")

Other data transformation and formatting operations, as well as many other general application tasks, are supported by a variety of packages in the tidyverse. For a full list of dependencies (as generated by rsconnect::appDependencies()), see the DEPENDENCIES file.

Data

Input data for the Shiny-iAtlas portal were accessed from multiple remote sources, including Synapse, the ISB Cancer Genomics Cloud, and Google Drive. For convenience, we have created locally cached versions of dataframe objects as feather files:

  • fmx_df.feather
  • feature_df.feather
  • feature_method_df.feather
  • im_direct_relationships.feather
  • im_potential_factors.feather
  • im_expr_df.feather
  • sample_group_df.feather

Methods

While many of the results presented in tables and plots are taken directly from IRWG data (including the main feature matrix and various feature and group annotations), we compute some values internally. Unless otherwise noted, the following methods/tools were used to compute summary statistics:

Correlation — Spearman's rank-order correlation:

stats::cor(x, y, method = "spearman", use = "pairwise.complete.obs")

Concordance Index (CI):

Concordance indexes for survival endpoints with respect to different immune readouts were computed using a custom package developed by Tai-Hsien Ou Yang at Columbia University. The concordanceIndex package includes a single synonymous function that can be used as follows:

concordanceIndex::concordanceIndex(predictions, observations)

... where predictions and observations are numerical vectors of the same length.

The concordanceIndex package can be installed from GitHub using devtools:

devtools::install_github("th86/concordanceIndex")

Local Shiny-iAtlas Session

To run the app locally, clone this repository and use the following command in the shiny-iatlas directory:

shiny::runApp()