update workflow and docs

Author: szcf-weiya

.githubs/workflows/ci.yml

@@ -0,0 +1,39 @@
+name: CI
+
+on: [push]
+
+jobs:
+  test-and-docs:
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04]
+        julia-version: ['1.9']
+        r-version: ['4.2.1']
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r-version }}
+
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+            
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          LD_LIBRARY_PATH: /opt/R/${{ matrix.r-version }}/lib/R/lib
+
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: lcov.info
+      - uses: julia-actions/julia-docdeploy@v1
+        if: ${{ matrix.os == 'ubuntu-22.04' && matrix.julia-version == '1.9' }} # only run docs in one env
+        env:
+          LD_LIBRARY_PATH: /opt/R/${{ matrix.r-version }}/lib/R/lib
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key

.gitignore

@@ -1,2 +1,3 @@
 Manifest.toml
-docs/build
+docs/build
+docs/src/examples/

docs/make.jl

@@ -20,6 +20,6 @@ makedocs(sitename="SplitClusterTest.jl",
         ]        
 )
 
-# deploydocs(
-#     repo = "github.com/szcf-weiya/SplitClusterTest.jl"
-# )
+deploydocs(
+    repo = "github.com/szcf-weiya/SplitClusterTest.jl"
+)

docs/src/examples/demo-mirror.md

@@ -4,16 +4,16 @@ using SplitClusterTest
 using Plots
 
 # Without cluster structure, the mirror statistics are symmetric about zero since all features are null features. 
-x, cl = gen_data_normal(1000, 2000, 0.5, prop_imp=0.1);
-ms = ds(x, method = "tstat", ret_ms = true)
+x, cl = gen_data_normal(1000, 2000, 0.0, prop_imp=0.1);
+ms = ds(x, ret_ms = true)
 histogram(ms, label = "")
 
 
 # With cluster structure, the mirror statistics of DE genes tend to be larger and away from null features, 
 # where the null features still exhibit a symmetric distribution about zero. 
 # Then we can properly take the cutoff to control the FDR, as shown by the red vertical line.
-x, cl = gen_data_normal(1000, 2000, 0.0, prop_imp=0.1);
-ms = ds(x, method = "tstat", ret_ms = true) # without vertical line
+x, cl = gen_data_normal(1000, 2000, 0.5, prop_imp=0.1);
+ms = ds(x, ret_ms = true) # without vertical line
 τ = calc_τ(ms)
 histogram(ms, label = "")
 Plots.vline!([τ], label = "", lw = 3)