Update vignette; reset R 4.0 as required minimum version

DESCRIPTION

@@ -19,7 +19,7 @@ Authors@R: c(person("Astrid", "Deschênes", email = "adeschen@hotmail.com",
     comment = c(ORCID = "0000-0002-0802-1071")))
 Encoding: UTF-8
 License: Artistic-2.0
-Depends: R (>= 3.5)
+Depends: R (>= 4.0)
 Imports: gprofiler2,
     strex,
     RCy3,

vignettes/gprofiler2cytoscape.Rmd

@@ -39,6 +39,8 @@ The `r Githubpkg("adeschen/gprofiler2cytoscape")` package and the underlying
 `r Githubpkg("adeschen/gprofiler2cytoscape")` code are distributed under the 
 Artistic license 2.0. You are free to use and redistribute this software. 
 
+<br>
+<br>
 
 # Citing
 
@@ -50,6 +52,8 @@ following:
   https://github.com/adeschen/gprofiler2cytoscape,
   https://adeschen.github.io/gprofiler2cytoscape/.
 
+<br>
+<br>
 
 # Introduction
 
@@ -89,7 +93,7 @@ _gprofiler2_ [@Kolberg2020]. The _gprofiler2_ package enables researchers to
 incorporate functional enrichment analysis into automated analysis pipelines 
 written in R. This greatly facilitates research reproducibility. 
 
-The `r Githubpkg("adeschen/gprofiler2cytoscape")` package enables the 
+The **_gprofiler2cytoscape_** package enables the 
 visualization of enrichment results generated by _gprofiler2_ as 
 customisable _Cytoscape_ network [@PaulShannon2003]. In the biological 
 networks generated by `r Githubpkg("adeschen/gprofiler2cytoscape")`, both 
@@ -111,42 +115,96 @@ Once the network is created, the user can personalize the visual attributes
 and integrate external information such as expression profiles, phenotypes 
 and other molecular states. The user can also peforms network analysis.
 
+<br>
+<br>
+
 # Installation
 
 To install the latest version accessible on the 
 `r Githubpkg("adeschen/gprofiler2cytoscape")` Github Website, the 
 `r CRANpkg("devtools")` package is required.
 
 ```{r installDemo01, eval=FALSE}
-## Load required package
-library(devtools)
-
 ## Install the latest version of gprofiler2cytoscape
+library(devtools)
 devtools::install_github('adeschen/gprofiler2cytoscape')
 ```
 
 It is also possible to install an official release. The list of available 
 releases is posted on the [gprofiler2cytoscape Release Website](https://github.com/adeschen/gprofiler2cytoscape/releases "gprofiler2cytoscape Release Site").
 
 ```{r installDemo02, eval=FALSE}
-## Load required package
-library(devtools)
-
 ## Install the version v0.1 of gprofiler2cytoscape
 ## using 'ref' parameter
-devtools::install_github('adeschen/gprofiler2cytoscape', ref = "v0.1")
+library(devtools)
+devtools::install_github('adeschen/gprofiler2cytoscape', ref = "v0.0.2")
 ```
 
-TODO
+<br>
+<br>
 
-# Transforming gprofiler2 enrichment results to Cytoscape network
 
+# Transforming gprofiler2 enrichment results to Cytoscape network
 
 
 ```{r graphListToGraph01, echo = FALSE, fig.align="left", fig.cap="From an enrichment list to a Cytoscape network", out.width = '100%'}
 knitr::include_graphics("FromListToGraph_v01.jpg")
 ```
 
+The following workflow gives an overview of the capabilities of 
+`r Githubpkg("adeschen/gprofiler2cytoscape")` 
+
+
+The key steps for the workflow are:
+
+Step                              | Function                    
+--------------------------------- | ---------------------------------------------
+ Doing an Enrichment analysis     | `gprofiler2::gost()`
+ Starting Cytoscape               |  outside R   
+ Create Cytoscape network         | `createNetwork()`
+
+The `package::function()` notation is used for functions from other packages.
+
+## Doing an Enrichment analysis 
+
+
+## Starting Cytoscape
+
+[Cytoscape](https://cytoscape.org/) is an open source software for 
+visualizing networks. It enables network integration with any type of attribute
+data. The Cytoscape software 
+is available at the [Cytoscape website](https://cytoscape.org/).
+
+```{r cytoscapeLogo01, echo = FALSE, fig.align="center", fig.cap="Cytoscape software logo.", out.width = '100%'}
+knitr::include_graphics("cy3sticker.png")
+```
+
+The Cytoscape network generated by 
+`r Githubpkg("adeschen/gprofiler2cytoscape")` 
+will be automatically loaded into the [Cytoscape](https://cytoscape.org/) 
+software when the application is running.
+
+If the application is not running, a CX JSON file will be created. The file 
+can then be loaded manually into the [Cytoscape](https://cytoscape.org/) 
+software.
+
+## Create Cytoscape network 
+
+TODO
+
+```{r runCreateNetwork, echo = TRUE, eval=FALSE}
+## Load demo gprofiler2 enrichment result
+data(demoGOST)
+
+## Create network for Gene Ontology - Molecular Function related results
+## The 'removeRoot=TRUE' parameter removes the root term from the network
+createNetwork(gostObject=demoGOST, source="GO:MF", removeRoot=FALSE,
+    title="GO Molecular Function Network")
+```
+
+<br>
+<br>
+
 # Session info
 
 Here is the output of sessionInfo() on the system on which this document 
@@ -157,6 +215,9 @@ sessionInfo()
 ```
 
 
+<br>
+<br>
+
 # References