From a1de274705fdaa1158d68c986e8a659e964c76c8 Mon Sep 17 00:00:00 2001 From: "Florian J. Auer" Date: Tue, 21 Dec 2021 22:58:21 +0100 Subject: [PATCH 1/3] Updated installation instructions --- README.md | 27 +++++++++++++++-- ...ementing_the_Cytoscape_Exchange_format.Rmd | 29 +++++++++++++++++-- 2 files changed, 50 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 7621b70..80baa27 100644 --- a/README.md +++ b/README.md @@ -106,10 +106,31 @@ Model](vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd) Installation ============ +For installing packages from github the `devtools` package is the most common approach. +However, it requires XML libraries installed on the system which can cause problems while installation due to unmet dependencies. +The `remotes` package covers the functionality to download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories without depending on XML libraries. +If `devtools` is already installed, of course it can be used, otherwise it is recommended to use the lightweight `remotes` package. + +**From github using remotes:** + +``` r +if(!"remotes" %in% installed.packages()){ + install.packages("remotes") +} +if(!"RCX" %in% installed.packages()){ + remotes::install_github("frankkramer-lab/RCX") +} +library(RCX) +``` + +**From github using devtools:** + ``` r -if (!"RCX" %in% installed.packages()) { - require(devtools) - install_github("frankkramer-lab/RCX") +if(!"devtools" %in% installed.packages()){ + install.packages("devtools") +} +if(!"RCX" %in% installed.packages()){ + devtools::install_github("frankkramer-lab/RCX") } library(RCX) ``` diff --git a/vignettes/RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd b/vignettes/RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd index a06b977..8da1f06 100644 --- a/vignettes/RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd +++ b/vignettes/RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd @@ -76,18 +76,41 @@ For an overview of the differences of the RCX implementation to the CX specifica # Installation +For installing packages from github the `devtools` package is the most common approach. +However, it requires XML libraries installed on the system which can cause problems while installation due to unmet dependencies. +The `remotes` package covers the functionality to download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories without depending on XML libraries. +If `devtools` is already installed, of course it can be used, otherwise it is recommended to use the lightweight `remotes` package. + +**From github using remotes:** + ```{r, eval=FALSE} +if(!"remotes" %in% installed.packages()){ + install.packages("remotes") +} if(!"RCX" %in% installed.packages()){ - require(devtools) - install_github("frankkramer-lab/RCX") + remotes::install_github("frankkramer-lab/RCX") } library(RCX) ``` +**From github using devtools:** -```{r installBioconductor, eval=FALSE, include=FALSE} +```{r, eval=FALSE} +if(!"devtools" %in% installed.packages()){ + install.packages("devtools") +} if(!"RCX" %in% installed.packages()){ + devtools::install_github("frankkramer-lab/RCX") +} +library(RCX) +``` + + +```{r installBioconductor, eval=FALSE, include=FALSE} +if(!"BiocManager" %in% installed.packages()){ install.packages("BiocManager") +} +if(!"RCX" %in% installed.packages()){ BiocManager::install("RCX") } library(RCX) From cf8688d1035f226479130e85187ead021b3a8a98 Mon Sep 17 00:00:00 2001 From: "Florian J. Auer" Date: Sat, 5 Feb 2022 03:05:11 +0100 Subject: [PATCH 2/3] Update README.md issue board --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 80baa27..28d2678 100644 --- a/README.md +++ b/README.md @@ -909,6 +909,14 @@ As igraph, graphNEL objects can not hold information about the visual representation of the network, so here too we can restore the original layout by adding the `CyVisualProperties` aspect we saved previously. +Errors, questions and suggestions +================================= + +If you have any questions to the usage of this package, suggestions for the further development of this package or encountered any problems in the process of the installation or while the usage: + +Pleas feel free to open a new [issue on our bord](https://github.com/frankkramer-lab/RCX/issues)! + + Session info ============ From 74ef70960d7e6c9495b3ee92387eeaedbeec0195 Mon Sep 17 00:00:00 2001 From: Andrew Chen <31497311+andrewdchen@users.noreply.github.com> Date: Tue, 26 Jul 2022 12:30:21 -0400 Subject: [PATCH 3/3] toigraph() conversion changes --- R/Igraph.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/Igraph.R b/R/Igraph.R index dc77893..1145a6f 100644 --- a/R/Igraph.R +++ b/R/Igraph.R @@ -184,8 +184,8 @@ toIgraph = function(rcx, directed=FALSE){ edges = rcx$edges ## reordering columns so that source and target are the first two edgeNames = colnames(edges) - edgeNames = c("source","target", - (edgeNames[!edgeNames %in% c("source","target")])) + edgeNames = c("s","t", + (edgeNames[!edgeNames %in% c("s","t")])) edges = edges[edgeNames] ## rename columns to use id as name nodes = rcx$nodes