kozo2

##' Import multiple KEGG pathways and integrate the pathways
##' into a cyjs file for Cy3D renderer
##'
##' @title Write cyjs file for transomics 3D visualization
##' @param pathwayID1 a KEGG pathway ID
##' @param pathwayID2 a KEGG pathway ID
##' @param pathwayID3 a KEGG pathway ID
##' @param zheight1 Z height for pathwayID1
##' @param zheight2 Z height for pathwayID2
##' @param zheight3 Z height for pathwayID3

kozo2

/content# xvfb-run -a ./cytoscape-unix-3.8.0/cytoscape.sh
karaf: JAVA_HOME not set; results may vary
karaf.base: /content/cytoscape-unix-3.8.0/framework
JAVA_HOME: null
             _
   ___ _   _| |_  ___  ___  ___  __ _ _ __   ___
  / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \
 | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/
  \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___|
       |___/                         |_|

kozo2

karaf: JAVA_HOME not set; results may vary
karaf.base: /content/cytoscape-unix-3.8.0/framework
JAVA_HOME: null
             _                                    
   ___ _   _| |_  ___  ___  ___  __ _ _ __   ___  
  / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ 
 | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/ 
  \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| 
       |___/                         |_|          

kozo2

---
title: "transomics2cytoscape"
author: "Kozo Nishida"
date: "2/26/2020"
package: transomics2cytoscape
output:
    BiocStyle::html_document
vignette: |
    %\VignetteIndexEntry{transomics2cytoscape}
    %\VignetteEngine{knitr::rmarkdown}

kozo2

library(dash)
library(dashCoreComponents)
library(dashHtmlComponents)
library(plotly)
#library(jsonlite)

app <- Dash$new()

app$layout(
  htmlDiv(

kozo2

Package: transomics2cytoscape
Type: Package
Title: Create 3D transomics network view with Çytoscape and Cy3D
Version: 0.99.0
Authors@R: person("Kozo", "Nishida", role = c("aut", "cre"),
    email = "[email protected]")
Depends: R (>= 3.6.0)
Imports: RCy3,
    BiocStyle,
    KEGGREST,

kozo2

10:00 - 12:00 ハッカソン 12:00 - 13:00 Lunch Break（所内食堂）

kozo2

kozo2

kozo2

root_node_df=getTableColumns('node')
root_edge_df=getTableColumns('edge')
# change networkforcus on GUI
gro_node_df=getTableColumns('node')
gro_edge_df=getTableColumns('edge')

new_node_df=bind_rows(roof_node_df, gro_node_df)
new_edge_df=bind_rows(roof_edge_df, gro_edge_df)

new_node_df %>% rename(id=SUID) -> foo