Deploying to gh-pages from @ 1a31fd4 🚀

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CaDrA
 Type: Package
 Title: Candidate Driver Analysis
-Version: 1.1.2
+Version: 1.0.2
 Date: 2022-11-20
 Authors@R: 
     c(person(given="Reina", family="Chau", role=c("aut","cre"), 

Dockerfile

@@ -10,33 +10,22 @@ FROM rocker/tidyverse:${R_VERSION} as base
 # Install system libraries of general use
 RUN apt-get update --allow-releaseinfo-change --fix-missing \
   && apt-get -y --no-install-recommends install \
-  tk \
+  apt-utils \
   libxtst6 \
   libxt6 \
-  ca-certificates \
-  git \
+  tk \
   && apt clean autoclean \
   && apt autoremove --yes \
   && rm -rf /var/lib/{apt,dpkg,cache,log}/
 
-# Build according to a specified release of CaDrA
-ARG CADRA_BRANCH
-ENV CADRA_BRANCH=${CADRA_BRANCH:-devel}
-
-# Set working directory to install CaDrA
-WORKDIR / 
-
-# Clone CaDrA repo
-RUN git clone https://github.com/montilab/CaDrA.git
-
-# Set working directory to CaDrA
-WORKDIR /CaDrA 
+# Create package directory 
+ENV PACKAGE_DIR=/CaDrA 
 
-# Checkout the desired branch for the build
-RUN git checkout ${CADRA_BRANCH} && git pull
+# Make package as working directory
+WORKDIR ${PACKAGE_DIR}
 
-# Install CaDrA denpendencies
-RUN Rscript "/CaDrA/install_r_packages.R"
+# Copy package code to Docker image
+COPY . ${PACKAGE_DIR}
 
 # Install all package dependencies
 RUN Rscript "${PACKAGE_DIR}/install_r_packages.R"

README.Rmd

@@ -67,7 +67,7 @@ BiocManager::install("SummarizedExperiment")
 
 # Usage
 
-Here, we are using a dataset of somatic mutations and CNAs extracted from the TCGA Breast Cancer Dataset. We will query this Feature Set based on an Input Score that measures the per-sample activity of YAP/TAZ (two important regulators of the hippo pathway). This score represents the projection on the TCGA BrCa dataset of a gene expression signature of YAP/TAZ knockdown derived in breast cancer cell lines. Our question of interest: what is the combination of genetic features [mutations and copy number alterations] that best “explain” the YAP/TAZ activity?
+Here, we are using a dataset of somatic mutations and CNAs extracted from the TCGA Breast Cancer Dataset. We will query this Feature Set based on an Input Score that measures the per-sample activity of YAP/TAZ (two important regulators of the hippo pathway). This score represents the projection on the TCGA BrCa dataset of a gene expression signature of YAP/TAZ knockdown derived in breast cancer cell lines. Our question of interest: what is the combination of genetic features (mutations and copy number alterations) that best “explain” the YAP/TAZ activity?
 
 ## (i) Load R packages
 
@@ -107,7 +107,7 @@ eset_mut_scna_flt <- CaDrA::prefilter_data(
 
 Here, we repeat the candidate search starting from each of the top 'N' features and report the combined results as a heatmap (to summarize the number of times each feature is selected across repeated runs). 
 
-IMPORTANT NOTE: The legacy function `topn_eval()` is equivalent to the new recommended `candidate_search()` function
+**IMPORTANT NOTE**: The legacy function `topn_eval()` is equivalent to the new recommended `candidate_search()` function.
 
 ```{r cadra}
 topn_res <- CaDrA::candidate_search(
@@ -124,7 +124,7 @@ topn_res <- CaDrA::candidate_search(
 )
 ```
 
-## (iv) Visualize results
+## (iv) Visualize the results
 
 ### Meta-feature plot
 
@@ -151,9 +151,9 @@ This plot is a heatmap of overlapping meta-features by repeating `candidate_sear
 CaDrA::topn_plot(topn_res) 
 ```
 
-# Additional guides
+# Additional Guides
 
-- [Run CaDrA within a Docker environment](https://montilab.github.io/CaDrA/articles/docker.html)
+- [How to run CaDrA within a Docker environment](https://montilab.github.io/CaDrA/articles/docker.html)
 
 # Acknowledgements
 

README.md

@@ -76,8 +76,8 @@ based on an Input Score that measures the per-sample activity of YAP/TAZ
 (two important regulators of the hippo pathway). This score represents
 the projection on the TCGA BrCa dataset of a gene expression signature
 of YAP/TAZ knockdown derived in breast cancer cell lines. Our question
-of interest: what is the combination of genetic features \[mutations and
-copy number alterations\] that best “explain” the YAP/TAZ activity?
+of interest: what is the combination of genetic features (mutations and
+copy number alterations) that best “explain” the YAP/TAZ activity?
 
 ## (i) Load R packages
 
@@ -119,8 +119,8 @@ Here, we repeat the candidate search starting from each of the top ‘N’
 features and report the combined results as a heatmap (to summarize the
 number of times each feature is selected across repeated runs).
 
-IMPORTANT NOTE: The legacy function `topn_eval()` is equivalent to the
-new recommended `candidate_search()` function
+**IMPORTANT NOTE**: The legacy function `topn_eval()` is equivalent to
+the new recommended `candidate_search()` function.
 
 ``` r
 topn_res <- CaDrA::candidate_search(
@@ -137,7 +137,7 @@ topn_res <- CaDrA::candidate_search(
 )
 ```
 
-## (iv) Visualize results
+## (iv) Visualize the results
 
 ### Meta-feature plot
 
@@ -172,9 +172,9 @@ CaDrA::topn_plot(topn_res)
 
 ![](./man/figures/summarize-1.png)<!-- -->
 
-# Additional guides
+# Additional Guides
 
-- [Run CaDrA within a Docker
+- [How to run CaDrA within a Docker
   environment](https://montilab.github.io/CaDrA/articles/docker.html)
 
 # Acknowledgements

_pkgdown.yml

@@ -61,7 +61,7 @@ navbar:
         href: articles/scoring_functions.html
       - text: "Permutation-Based Testing"
         href: articles/permutation_based_testing.html
-      - text: "Run CaDrA within a Docker Environment"
+      - text: "How to run CaDrA within a Docker Environment"
         href: articles/docker.html
     - text: "Reference"
       href: reference/index.html

docker-compose.yml

@@ -4,20 +4,19 @@ x-r-version:
   &r-version
   R_VERSION=4.3.0
 
-x-cadra-branch:
-  &cadra-branch
-  CADRA_BRANCH=devel
-  
+x-cadra-git-repo:
+  &cadra-git-repo
+  https://github.com/montilab/CaDrA.git
+
 services:
   cadra:
     container_name: cadra
     image: montilab/cadra:latest
     build: 
-      context: https://github.com/montilab/CaDrA.git
+      context: *cadra-git-repo
       dockerfile: Dockerfile
       args:
         - *r-version
-        - *cadra-branch
     restart: always
     ports:
       - 8787:8787