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@@ -1,54 +0,0 @@

-title: "Cytoscape Formatting"

-author: "Shana White"

-date: "`r Sys.Date()`"

-output: rmarkdown::html_vignette

-vignette: >

-    %\VignetteIndexEntry{KEGGlincs Workflows}

-    %\VignetteEngine{knitr::rmarkdown}

-    %\VignetteEncoding{UTF-8}

-

-##Manually format pathway maps for convenient viewing and proper node size

-The following two steps must be followed to reproduce the pathway maps as seen

-in the workflows for users without RCy3 available on their system.  If RCy3 is

-available, please use the functions `cyto_vis_auto` and `KEGG_lincs_auto` 

-from https://github.com/uc-bd2k/KEGGlincs/blob/master/R/cyto_vis_auto.R and

-https://github.com/uc-bd2k/KEGGlincs/blob/master/R/KEGG_lincs_auto.R. 

-

-Otherwise please follow the steps outlined below.

-

-### 1) Autofit content to window

-

-```{r autofit,eval=TRUE,echo=FALSE,out.width=800}

-knitr::include_graphics("image_files/fit_content.jpg")

-```

-

-### 2) 'Re-lock' the node width and height

-Neither this package's author nor other collaborators working on similar 

-projects using Cytoscape via cyREST understand why this step is neccessary.

-

-First, locate the 'Style' tab under the Control Panel

-

-```{r locate_style,eval=TRUE,echo=FALSE,out.width=800}

-knitr::include_graphics("image_files/select_style_tab.jpg")

-```

-

-Then, scroll down [if needed] to the bottom of the window and locate the box

-labelled "Lock node width and height".  

-

-```{r find_box,eval=TRUE,echo=FALSE,out.width=800}

-knitr::include_graphics("image_files/find_box.jpg")

-```

-

-The box should be checked; uncheck the box, then re-check it - the nodes should

-then convert to their intended width/height format.

-

-##Modify the threshold to label edges even if desired pathway has many edges

-

-If a pathway has a large number of edges (for example the Fox0 pathway 

-showcased in Workflow 1), users can adjust Cytoscape settings to render the 

-edge labels by selecting following the path Edit > Preferences > Properties and

-selecting render.edgeLabelThreshold.  Click 'Modify' and increase the value as

-desired [or until edge labels become visible].  The default setting in 

-Cytoscape is 200.

@@ -163,15 +163,6 @@ edges connecting nodes) or have not been hard-coded in the KGML file.  The node

 labels may also differ between maps (KEGGlincs labels nodes as the first 'alias'

 in the respective KGML slot as there is no corresponding 'label' slot).

-*Note: to have the pathway maps automatically formatted for convenient viewing

-and proper node size, please use the function `cyto_vis_auto`:

-https://github.com/uc-bd2k/KEGGlincs/blob/master/R/cyto_vis_auto.R

-This function requires systems to have the R package RCy3 installed, which is 

-not yet available for all systems.

-

-Otherwise please follow the steps under `CytoscapeSettings.Rmd` to reproduce 

-the maps generated in this vignette.

-

 #####Alternative: KEGG_lincs master function

 The steps above may be avoided if the user does not wish to generate 

 intermediary files/objects by making use of the function  `KEGG_lincs` as 

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