Update github actions with magick

fbertran · Mar 21, 2021 · 2b7fc83 · 2b7fc83
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -23,6 +23,12 @@ jobs:
       - name: Install XQuartz on macOS
         if: runner.os == 'macOS'
         run: brew install xquartz --cask
+      - name: Install ghostscript on macOS
+        if: runner.os == 'macOS'
+        run: brew install ghostscript
+      - name: Install Magick on macOS
+        if: runner.os == 'macOS'
+        run: brew install imagemagick
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "rcmdcheck"))

diff --git a/README.Rmd b/README.Rmd
@@ -56,37 +56,6 @@ The weights are viewed as a penalty factors in the penalized regression model: i
 
 
 
-![Infered F matrix of the network (General shape).](docs/reference/figures/README-Fresults-1.png)
-
-
-
-![Infered coefficient matrix of the network (General shape).](docs/reference/figures/README-heatresults-1.png)
-
-
-
-![Infered F matrix of the network (cascade shape).](docs/reference/figures/README-FresultsLC-1.png)
-
-
-
-![Infered coefficient matrix of the network (cascade shape).](docs/reference/figures/README-heatresultsLC-1.png)
-
-
-
-![Reverse-engineered network.](docs/reference/figures/README-plotnet2-1.png)
-
-
-
-![Evolution of a reverse-engineered network with increasing cut-off values.](docs/reference/animation.gif)
-
-
-
-![Plot of simulated data for cascade networks featuring cluster membership.](docs/reference/figures/README-plotsimuldata-1.png)
-
-
-
-![Plot of simulated data for cascade networks featuring subject membership.](docs/reference/figures/README-plotsimuldata-2.png)
-
-
 A word for those that have been using our seminal work, the `Cascade` package that we created several years ago and that was a very efficient network reverse engineering tool for cascade networks 
 (Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014), <https://doi.org/10.1093/bioinformatics/btt705>, <https://cran.r-project.org/package=Cascade>, <https://github.com/fbertran/Cascade> and <https://fbertran.github.io/Cascade/>).
 
@@ -512,12 +481,12 @@ destdir = "~/Github/Patterns/docs/reference/evolution/"
 evolution(network,sequence,type.ani = "gif",outdir=destdir)
 evolution(network,sequence,type.ani = "html",outdir=destdir)
 ```
-![Evolution as .gif.](docs/reference/evolution/animation.gif)
+![Evolution as .gif.](https://fbertran.github.io/Patterns/reference/evolution/animation.gif)
 
-[Evolution as .html.](docs/reference/evolution/index.html)
+[Evolution as .html.](https://fbertran.github.io/Patterns/reference/evolution/index.html)
 
 Evolution of some properties of a reverse-engineered network with increasing cut-off values.
-![Evolution of some properties of a reverse-engineered network with increasing cut-off values.](docs/reference/compare-methods-1.png)
+![Evolution of some properties of a reverse-engineered network with increasing cut-off values.](https://fbertran.github.io/Patterns/reference/compare-methods-1.png)
 
 We switch to data that were derived from the inferrence of a real biological network and try to detect the optimal cutoff value: the best cutoff value for a network to fit a scale free network. The `cutoff` was validated only single group cascade networks (number of actors groups = number of timepoints) and for genes dataset. Instead of the `cutoff` function, manual curation or the stability selection or the selectboost algorithm should be used.
 
@@ -598,4 +567,36 @@ This process could be improved by retrieve a real gene_ID using the `bitr` funct
 
 
 
+### Examples of outputs
+
+![Infered F matrix of the network (General shape).](https://fbertran.github.io/Patterns/reference/figures/README-Fresults-1.png)
+
+
+
+![Infered coefficient matrix of the network (General shape).](https://fbertran.github.io/Patterns/reference/figures/README-heatresults-1.png)
+
+
+
+![Infered F matrix of the network (cascade shape).](https://fbertran.github.io/Patterns/reference/figures/README-FresultsLC-1.png)
+
+
+
+![Infered coefficient matrix of the network (cascade shape).](https://fbertran.github.io/Patterns/reference/figures/README-heatresultsLC-1.png)
+
+
+
+![Reverse-engineered network.](https://fbertran.github.io/Patterns/reference/figures/README-plotnet2-1.png)
+
+
+
+![Evolution of a reverse-engineered network with increasing cut-off values.](https://fbertran.github.io/Patterns/reference/evolution/animation.gif)
+
+
+
+![Plot of simulated data for cascade networks featuring cluster membership.](https://fbertran.github.io/Patterns/reference/figures/README-plotsimuldata-1.png)
+
+
+
+![Plot of simulated data for cascade networks featuring subject membership.](https://fbertran.github.io/Patterns/reference/figures/README-plotsimuldata-2.png)
+
 
diff --git a/README.md b/README.md
@@ -47,37 +47,6 @@ The weights are viewed as a penalty factors in the penalized regression model: i
 
 
 
-![Infered F matrix of the network (General shape).](docs/reference/figures/README-Fresults-1.png)
-
-
-
-![Infered coefficient matrix of the network (General shape).](docs/reference/figures/README-heatresults-1.png)
-
-
-
-![Infered F matrix of the network (cascade shape).](docs/reference/figures/README-FresultsLC-1.png)
-
-
-
-![Infered coefficient matrix of the network (cascade shape).](docs/reference/figures/README-heatresultsLC-1.png)
-
-
-
-![Reverse-engineered network.](docs/reference/figures/README-plotnet2-1.png)
-
-
-
-![Evolution of a reverse-engineered network with increasing cut-off values.](docs/reference/animation.gif)
-
-
-
-![Plot of simulated data for cascade networks featuring cluster membership.](docs/reference/figures/README-plotsimuldata-1.png)
-
-
-
-![Plot of simulated data for cascade networks featuring subject membership.](docs/reference/figures/README-plotsimuldata-2.png)
-
-
 A word for those that have been using our seminal work, the `Cascade` package that we created several years ago and that was a very efficient network reverse engineering tool for cascade networks 
 (Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014), <https://doi.org/10.1093/bioinformatics/btt705>, <https://cran.r-project.org/package=Cascade>, <https://github.com/fbertran/Cascade> and <https://fbertran.github.io/Cascade/>).
 
@@ -1419,12 +1388,12 @@ evolution(network,sequence,type.ani = "html", outdir=getwd())
 #> Error in setwd(outdir): impossible de changer de répertoire de travail
 #> Error in setwd(outdir): impossible de changer de répertoire de travail
 ```
-![Evolution as .gif.](docs/reference/evolution/animation.gif)
+![Evolution as .gif.](https://fbertran.github.io/Patterns/reference/evolution/animation.gif)
 
-[Evolution as .html.](docs/reference/evolution/index.html)
+[Evolution as .html.](https://fbertran.github.io/Patterns/reference/evolution/index.html)
 
 Evolution of some properties of a reverse-engineered network with increasing cut-off values.
-![Evolution of some properties of a reverse-engineered network with increasing cut-off values.](docs/reference/compare-methods-1.png)
+![Evolution of some properties of a reverse-engineered network with increasing cut-off values.](https://fbertran.github.io/Patterns/reference/compare-methods-1.png)
 
 We switch to data that were derived from the inferrence of a real biological network and try to detect the optimal cutoff value: the best cutoff value for a network to fit a scale free network. The `cutoff` was validated only single group cascade networks (number of actors groups = number of timepoints) and for genes dataset. Instead of the `cutoff` function, manual curation or the stability selection or the selectboost algorithm should be used.
 
@@ -1736,4 +1705,36 @@ This process could be improved by retrieve a real gene_ID using the `bitr` funct
 
 
 
+### Examples of outputs
+
+![Infered F matrix of the network (General shape).](https://fbertran.github.io/Patterns/reference/figures/README-Fresults-1.png)
+
+
+
+![Infered coefficient matrix of the network (General shape).](https://fbertran.github.io/Patterns/reference/figures/README-heatresults-1.png)
+
+
+
+![Infered F matrix of the network (cascade shape).](https://fbertran.github.io/Patterns/reference/figures/README-FresultsLC-1.png)
+
+
+
+![Infered coefficient matrix of the network (cascade shape).](https://fbertran.github.io/Patterns/reference/figures/README-heatresultsLC-1.png)
+
+
+
+![Reverse-engineered network.](https://fbertran.github.io/Patterns/reference/figures/README-plotnet2-1.png)
+
+
+
+![Evolution of a reverse-engineered network with increasing cut-off values.](https://fbertran.github.io/Patterns/reference/evolution/animation.gif)
+
+
+
+![Plot of simulated data for cascade networks featuring cluster membership.](https://fbertran.github.io/Patterns/reference/figures/README-plotsimuldata-1.png)
+
+
+
+![Plot of simulated data for cascade networks featuring subject membership.](https://fbertran.github.io/Patterns/reference/figures/README-plotsimuldata-2.png)
+
 
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   ExampleCLL: ExampleCLL.html
   IntroPatterns: IntroPatterns.html
-last_built: 2021-03-21T00:17Z
+last_built: 2021-03-21T01:04Z