Update readme to fix urls

fbertran · Mar 21, 2021 · d2d984d · d2d984d
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diff --git a/.gitignore b/.gitignore
@@ -25,4 +25,4 @@ Meta
 
 # User-specific files
 .Ruserdata
-doc
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -54,7 +54,7 @@ Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
 Description: A modeling tool dedicated to biological network modeling (Bertrand and others 2020, <doi:10.1093/bioinformatics/btaa855>). It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks (Jung and others 2014, <doi:10.1093/bioinformatics/btt705>). Example of use with microarray or RNA-Seq data are provided.
 License: GPL (>= 2)
 Encoding: UTF-8
-Collate: Patterns-package.R datasets.R global.R micro_array.R network.R micro_array-network.R
+Collate: Patterns-package.R global.R datasets.R micro_array.R network.R micro_array-network.R
 	micropredict.R
 Classification/MSC: 62J05, 62J07, 62J99, 92C42
 VignetteBuilder: knitr

diff --git a/Patterns.Rproj b/Patterns.Rproj
@@ -16,6 +16,6 @@ BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageCheckArgs: --as-cran
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd
 
 QuitChildProcessesOnExit: Yes
diff --git a/README.Rmd b/README.Rmd
@@ -76,7 +76,7 @@ The weights are viewed as a penalty factors in the penalized regression model: i
 
 
 
-![Evolution of a reverse-engineered network with increasing cut-off values.](docs/reference/evolution/animation.gif)
+![Evolution of a reverse-engineered network with increasing cut-off values.](docs/reference/animation.gif)
 
 
 
@@ -494,7 +494,7 @@ Heatmap of the coefficients of the Omega matrix of the network
 stats::heatmap(Net_inf_P_SelectBoostWeighted@network, Rowv = NA, Colv = NA, scale="none", revC=TRUE)
 ```
 
-###Post inference network analysis
+### Post inference network analysis
 Such an analysis is only required if the model was not fitted using the stability selection or the selectboost algorithm.
 
 Create an animation of the network with increasing cutoffs with an animated .gif format or a  html webpage in the working directory.

diff --git a/README.md b/README.md
@@ -67,7 +67,7 @@ The weights are viewed as a penalty factors in the penalized regression model: i
 
 
 
-![Evolution of a reverse-engineered network with increasing cut-off values.](docs/reference/evolution/animation.gif)
+![Evolution of a reverse-engineered network with increasing cut-off values.](docs/reference/animation.gif)
 
 
 
@@ -285,9 +285,10 @@ Plot the simulated network.
 
 ```r
 Patterns::plot(Net, choice="network")
-#> Error: 'plot' is not an exported object from 'namespace:Patterns'
 ```
 
+<img src="man/figures/README-plotnet1-1.png" title="plot of chunk plotnet1" alt="plot of chunk plotnet1" width="100%" />
+
 If a gene clustering is known, it can be used as a coloring scheme.
 
 ```r
@@ -308,9 +309,10 @@ Plot the F matrix using the `pixmap` package, for high dimensional F matrices.
 
 ```r
 plot(Net, choice="Fpixmap")
-#> Error in as.double(y): cannot coerce type 'S4' to vector of type 'double'
 ```
 
+<img src="man/figures/README-plotFpixmap-1.png" title="plot of chunk plotFpixmap" alt="plot of chunk plotFpixmap" width="100%" />
+
 We simulate gene expression according to the network that was previously drawn
 
 ```r
@@ -1331,8 +1333,6 @@ Net_inf_P_SelectBoost <- Patterns::inference(M, Finit=CascadeFinit(4,4), Fshape=
 
 
 ```
-#> Warning: 'Patterns' namespace cannot be unloaded:
-#>   tentative d'obtenir le slot "defined" d'un objet d'une classe élémentaire ("environment") sans slots
 #> 
 #> Attaching package: 'Patterns'
 #> The following object is masked from 'package:igraph':
@@ -1403,7 +1403,7 @@ stats::heatmap(Net_inf_P_SelectBoostWeighted@network, Rowv = NA, Colv = NA, scal
 
 <img src="man/figures/README-heatresultsSBW-1.png" title="plot of chunk heatresultsSBW" alt="plot of chunk heatresultsSBW" width="100%" />
 
-###Post inference network analysis
+### Post inference network analysis
 Such an analysis is only required if the model was not fitted using the stability selection or the selectboost algorithm.
 
 Create an animation of the network with increasing cutoffs with an animated .gif format or a  html webpage in the working directory.
@@ -1421,7 +1421,7 @@ evolution(network,sequence,type.ani = "html", outdir=getwd())
 ```
 ![Evolution as .gif.](docs/reference/evolution/animation.gif)
 
-[Evolution as .html.](reference/evolution/index.html)
+[Evolution as .html.](docs/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)

diff --git a/docs/articles/ExampleCLL.html b/docs/articles/ExampleCLL.html
diff --git a/docs/articles/ExampleCLL_files/figure-html/plotTFinsel2-1.png b/docs/articles/ExampleCLL_files/figure-html/plotTFinsel2-1.png
diff --git a/docs/authors.html b/docs/authors.html
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: 2021-03-20T10:23Z
+last_built: 2021-03-21T00:17Z
 
diff --git a/docs/reference/evolution/Rplot1.png b/docs/reference/evolution/Rplot1.png
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