CorDiffViz

Code for estimating and visualizing differential correlation matrices for two samples.

Installation

Run the following lines in R.

install.packages("devtools")
devtools::install_github("sqyu/CorDiffViz")

What this package does

Sparsely estimates and visualizes

cor(dat1) - cor(dat2)

(self correlations), or

cor(dat1X, dat1Y) - cor(dat2X, dat2Y)

(cross correlations) with thresholds determined by parametric tests, permutation tests, and the test from Cai and Zhang (2016).

Usage

Install the R package, and in R call the

CorDiffViz::viz()

function on the data matrices; an example is given here. For the arguments of the function, consult the R documentation by calling?CorDiffViz::viz.

After the R code finishes running, you can open viz.html in your current R working directory from your local browser for visualizations of the estimates. Although less interesting, the plots folder contains some static graphs and heatmaps for your reference.

If you manually changed the auto-generated files

After calling CorDiffViz::viz() to do the estimation, the visualization file viz.html and the generated data should automatically be in your current working directory in R. Just open it to see the visualizations and nothing else needs to be done.

If you for some reason changed the names or deleted some of the generated files, you may need to read the following.

 📂my_experiment_folder
 ┣ 📜viz.html
 ┣ 📂scripts
 ┃ ┗ 📜.js files and style.css
 ┣ 📂dats
 ┃ ┣ 📂my_data_self_correlations
 ┃ ┃ ┗ 📜.json files
 ┃ ┣ 📂my_data_X1:15_Y16:35_correlations
 ┃ ┃ ┗ 📜.json files
 ┃ ┗ 📂estimates_for_another_data
 ┃   ┗ 📜.json files
 ┗ 📂plots
   ┣ 📂my_data_self_correlations
   ┣ 📂my_data_X1:15_Y16:35_correlations
   ┗ 📂estimates_for_another_data

The viz.html file you are trying to open and its auxiliary scripts folder must be in the same folder (my_experiment_folder above) as the auto-generated dats folder. The dats folder contains sub-folders with names provided by you as the dat_name argument to CorDiffViz::viz(), and each sub-folder represents one dataset/set of estimates.

If you delete some of the sub-folders in dats or change their names you must run CorDiffViz::setup_js_html() from the directory that contains viz.html, scripts and dats, i.e. from my_experiment_folder in the example above.

Similarly, if for some reason your viz.html and scripts are missing, simply run CorDiffViz::setup_js_html() from the folder where dats lies, i.e. from my_experiment_folder in the example above.