ShinyGATOM -> shinyGatom

Author: assaron

NAMESPACE

@@ -1,9 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
-export(ShinyGATOM)
+export(shinyGatom)
 import("BioNet")
 import(RCurl)
 import(data.table)
+import(fgsea)
 import(gatom)
 import(igraph)
 import(logging)

R/app.R

@@ -1,7 +1,4 @@
-# load_all("/home/masha/Research/RCode/RShiny/shinyCyJS")
-
-
-#' starts shiny GATOM application
+#' starts Shiny GATOM application
 #' @import shiny
 #' @import data.table
 #' @import gatom
@@ -14,9 +11,9 @@
 #' @import fgsea
 #' @import markdown
 #' @export
-ShinyGATOM <- function(config_file=system.file('config.yml', package = 'ShinyGATOM')) {
+shinyGatom <- function(config_file=system.file('config.yml', package = 'shinyGatom')) {
     addResourcePath('/www',
-                    system.file('www', package = 'ShinyGATOM'))
+                    system.file('www', package = 'shinyGatom'))
 
     shinyApp(app_ui(config_file), app_server(config_file))
 }

R/app_server.R

@@ -170,6 +170,7 @@ app_server <- function(config_file) {
             gene.de.meta <- getGeneDEMeta(gene.de.raw, org.gatom.anno)
 
             res <- prepareDE(gene.de.raw, gene.de.meta)
+            res[, signalRank := NULL] # todo
 
             logdebug(capture.output(str(res)))
             if (!all(necessary.gene.de.fields %in% names(res))) {

R/app_ui.R

@@ -210,10 +210,10 @@ app_ui <- function(config_file) {
 
     helpPanel <- fixedRow(
         mainPanel(id="helpPanel",
-                  includeMarkdown(system.file("help.markdown", package="ShinyGATOM"))))
+                  includeMarkdown(system.file("help.markdown", package="shinyGatom"))))
 
     aboutPanel <- fixedRow(
-        mainPanel(includeMarkdown(system.file("about.markdown", package="ShinyGATOM"))))
+        mainPanel(includeMarkdown(system.file("about.markdown", package="shinyGatom"))))
 
     fluidPage(
         fluidPage(
@@ -224,11 +224,11 @@ app_ui <- function(config_file) {
                 #tags$script(src="www/d3.v3.js"),
                 tags$script(src="www/gam.js"),
                 tags$link(rel="stylesheet", href="www/gam.css"),
-                includeScript(system.file("ga.js", package="ShinyGATOM")),
+                includeScript(system.file("ga.js", package="shinyGatom")),
                 tags$title("Shiny GATOM")
             ),
 
-            includeHTML(system.file("misc.xhtml", package="ShinyGATOM")),
+            includeHTML(system.file("misc.xhtml", package="shinyGatom")),
             div(id="updateEsParameters", class="js-output"),
 
             titlePanel("Shiny GATOM: integrated analysis of genes and metabolites"),

app.R

@@ -1,4 +1,4 @@
 # for compatibility with Shiny Server
 pkgload::load_all(export_all = FALSE, helpers = FALSE, attach_testthat = FALSE)
-ShinyGATOM::ShinyGATOM()
+shinyGatom::shinyGatom()
 

inst/www/img/data_summary.png

@@ -17,7 +17,7 @@ Sys.setenv("CPLEX_HOME"="/home/masha/cplex")
 
 ## Running app
 load_all()
-ShinyGATOM()
+shinyGatom()
 
 
 ## Testing

inst/www/img/module.png

@@ -1,4 +1,4 @@
 library(testthat)
-library(ShinyGATOM)
+library(shinyGatom)
 
-test_check("ShinyGATOM")
+test_check("shinyGatom")

man/ShinyGATOM.Rd

@@ -8,7 +8,7 @@ example.gene.de <- gene.de.rawEx
 data("met.kegg.dbEx")
 met.kegg.db <- met.kegg.dbEx
 
-conf <- config::get(file=system.file('config.yml', package = 'ShinyGATOM'),
+conf <- config::get(file=system.file('config.yml', package = 'shinyGatom'),
                     use_parent = FALSE)
 
 test_that("lazyReadRDS works with remote files", {
@@ -21,23 +21,23 @@ test_that("lazyReadRDS works with remote files", {
 
 
 test_that("Node attributes are created", {
-    load(system.file('testdata/moduleEx.Rda', package = 'ShinyGATOM'))
+    load(system.file('testdata/moduleEx.Rda', package = 'shinyGatom'))
     vertex.table <- as_data_frame(module, what="vertices")
     res <- getJsNodeStyleAttributes(vertex.table)
     expect_true(!is.null(res$tooltip))
 })
 
 
 test_that("Edge attributes are created", {
-    load(system.file('testdata/moduleEx.Rda', package = 'ShinyGATOM'))
+    load(system.file('testdata/moduleEx.Rda', package = 'shinyGatom'))
     edge.table <- as_data_frame(module, what="edges")
     res <- getJsEdgeStyleAttributes(edge.table)
     expect_true(!is.null(res$tooltip))
 })
 
 
 test_that("ShinyCyJs data is created", {
-    load(system.file('testdata/moduleEx.Rda', package = 'ShinyGATOM'))
+    load(system.file('testdata/moduleEx.Rda', package = 'shinyGatom'))
     res <- prepareForShinyCyJS(module)
     expect_true(!is.null(res))
 })

run.R

@@ -9,13 +9,13 @@ library(shiny)
 # Sys.setenv("GATOM_LOCAL_DATA"="/home/masha/Research/RCode/RShiny/data")
 # Sys.setenv("CPLEX_HOME"="/home/masha/cplex")
 
-conf <- config::get(file=system.file('config.yml', package = 'ShinyGATOM'),
+conf <- config::get(file=system.file('config.yml', package = 'shinyGatom'),
                     use_parent = FALSE)
 
 
 ## Data is loaded & annotated with KEGG network
 context("Data loads & annotates with KEGG network")
-testServer(ShinyGATOM(), {
+testServer(shinyGatom(), {
     session$setInputs(loadExampleGeneDE = TRUE)
     session$setInputs(loadExampleMetDE = TRUE)
     session$setInputs(loadExampleLipidDE = FALSE)
@@ -27,27 +27,27 @@ testServer(ShinyGATOM(), {
 
 ## Data is read & annotated with KEGG network
 context("Data is read & annotated with KEGG network")
-testServer(ShinyGATOM(), {
+testServer(shinyGatom(), {
     session$setInputs(loadExampleGeneDE = FALSE)
     session$setInputs(loadExampleMetDE = FALSE)
     session$setInputs(loadExampleLipidDE = FALSE)
-    
+
     session$setInputs(network = "kegg")
     session$setInputs(organism = "mmu")
     session$setInputs(nodesAs = "atoms")
-    
-    session$setInputs(geneDE=data.frame(datapath=conf$example.gene.de.path, 
+
+    session$setInputs(geneDE=data.frame(datapath=conf$example.gene.de.path,
                                         name="Ctrl.vs.MandLPSandIFNg.met.de.tsv"))
-    session$setInputs(metDE=data.frame(datapath=conf$example.met.de.path, 
+    session$setInputs(metDE=data.frame(datapath=conf$example.met.de.path,
                                        name="Ctrl.vs.MandLPSandIFNg.met.de.tsv"))
-    
+
     expect_equal(metIdsType(), "HMDB")
 })
 
 
 ## Data is loaded & annotated with Rhea network
 context("Data is loaded & annotated with Rhea network")
-testServer(ShinyGATOM(), {
+testServer(shinyGatom(), {
     session$setInputs(loadExampleGeneDE = TRUE)
     session$setInputs(loadExampleMetDE = TRUE)
     session$setInputs(loadExampleLipidDE = FALSE)
@@ -59,7 +59,7 @@ testServer(ShinyGATOM(), {
 
 ## Network is created with KEGG network and nodes as atoms
 context("Network is created with KEGG network and nodes as atoms")
-testServer(ShinyGATOM(), {
+testServer(shinyGatom(), {
     session$setInputs(loadExampleGeneDE = TRUE)
     session$setInputs(loadExampleMetDE = TRUE)
     session$setInputs(loadExampleLipidDE = FALSE)
@@ -76,7 +76,7 @@ testServer(ShinyGATOM(), {
 
 ## Network is created with Rhea network and nodes as metabolites
 context("Network is created with Rhea network and nodes as metabolites")
-testServer(ShinyGATOM(), {
+testServer(shinyGatom(), {
     session$setInputs(loadExampleGeneDE = TRUE)
     session$setInputs(loadExampleMetDE = TRUE)
     session$setInputs(loadExampleLipidDE = FALSE)
@@ -90,10 +90,30 @@ testServer(ShinyGATOM(), {
     expect_true(!is.null(V(g)))
 })
 
+testServer(shinyGatom(), {
+    session$setInputs(loadExampleGeneDE = FALSE)
+    session$setInputs(loadExampleMetDE = FALSE)
+    session$setInputs(loadExampleLipidDE = FALSE)
+
+    session$setInputs(network = "kegg")
+    session$setInputs(organism = "hsa")
+    session$setInputs(nodesAs = "metabolites")
+
+    session$setInputs(geneDE=data.frame(datapath="https://artyomovlab.wustl.edu/publications/supp_materials/GAM/MCF10A.Ctrl.vs.2DG.gene.de.tsv",
+                                        name="MCF10A.Ctrl.vs.2DG.gene.de.tsv"))
+
+    session$setInputs(preprocess = TRUE)
+    session$setInputs(runStep1 = "click")
+
+    g <- gInput()
+    expect_true(!is.null(V(g)))
+})
+
+
 
 # ## Module is found
 # context("Module is found")
-# testServer(ShinyGATOM(), {
+# testServer(shinyGatom(), {
 #     session$setInputs(loadExampleGeneDE = TRUE)
 #     session$setInputs(loadExampleMetDE = TRUE)
 #     session$setInputs(network = "kegg")
@@ -121,4 +141,4 @@ testServer(ShinyGATOM(), {
 # })
 
 
-# context("")
+# context("")