version 0.1.2

DESCRIPTION

@@ -1,15 +1,16 @@
 Package: RnavGraph
 Type: Package
 Title: Using graphs as a navigational infrastructure.
-Version: 0.1.1
-Date: 2011-06-02
+Version: 0.1.2
+Date: 2012-02-15
 Author: Adrian R. Waddell and R. Wayne Oldford
 Maintainer: Adrian Waddell <adrian@waddell.ch>
-Url: http://adrian.waddell.ch/
-Description: GUI to explore high dimensional data (including image data) using graphs as navigational infrastructure.
+Url: http://www.navgraph.com
+Description: GUI to explore high dimensional data (including image
+        data) using graphs as navigational infrastructure.
 License: GPL-2
 Suggests: PairViz, scagnostics, rgl, grid, MASS, rggobi, RGtk2, hexbin,
-        RDRToolbox, vegan, RnavGraphImageData
+        RDRToolbox, vegan, RnavGraphImageData, png, Rgraphviz
 Depends: R (>= 2.10.0), methods, graphics, tcltk, graph
 Imports: RBGL
 LazyLoad: yes
@@ -19,6 +20,6 @@ Collate: 'AllGenerics.R' 'ng_data.R' 'ng_graph.R' 'ng_path.R'
         'Viz2D_Ggobi.R' 'Viz2D_Axis.R' 'Viz2D_tk2d.R'
         'FunctionNavGraph.R' 'graphtools.R' 'navGraph.R' 'scagNav.R'
         'zzz.R'
-Packaged: 2011-11-22 01:59:52 UTC; adrian
+Packaged: 2012-02-17 12:21:03 UTC; adrian
 Repository: CRAN
-Date/Publication: 2011-11-22 08:45:17
+Date/Publication: 2012-02-17 17:18:29

MD5

@@ -1,26 +1,26 @@
-42dc70d45183cffaafcc0cd963eba5e1 *DESCRIPTION
-50e6aceaaa33f68dcec63bd0ed69a5d8 *NAMESPACE
-f5d9a0d1efd0b8b7a88badc92b4f9e89 *NEWS
-975561750ebf517d442103758808f5a2 *R/AllGenerics.R
-3a89d7085371482989bccc875f252add *R/FunctionNavGraph.R
+b1c74de1902019922b72646a074be1ec *DESCRIPTION
+c2013f30dbf0baba1aaccacd9a1f38d5 *NAMESPACE
+13488fab8b0813269a3ecdef9a60d9c9 *NEWS
+2eb21102bd24f42a9eaa379c87aa36e3 *R/AllGenerics.R
+1eae90f5511b1e0227466cecb11e61a3 *R/FunctionNavGraph.R
 698183f7c8d7f656c8bda9b23251958c *R/GraphDisplay.R
 f9a01a193c02ca5efb88ba0d1fd59177 *R/NavGraphHandler.R
 ac0fed0cfde2f72b087b418fa6329b6d *R/SettingClasses.R
 8649cdcb75fe57d033c1d101f23fc3a2 *R/Visualization.R
-af44c988350f0246a2168dffd1b8f42c *R/Visualization2D.R
-d4b275be83045e7a2f8c998325e04a42 *R/Viz2D_Axis.R
-f7826c4d8da66784814b901cb4ddd5b5 *R/Viz2D_Ggobi.R
-b8456e92af433a96f13c7d1592c320fd *R/Viz2D_tk2d.R
+7d9997dc3daab26a86ab10ff3568abab *R/Visualization2D.R
+c023105f8b05388c4f44f5e8c119075b *R/Viz2D_Axis.R
+1a7596ce73f61df0bec6bec0b02001eb *R/Viz2D_Ggobi.R
+07c4c9bc26f167109e3a90e7c949cfdc *R/Viz2D_tk2d.R
 61f8b9c6b01a6ebe5c5c0da86e9fbd37 *R/graphtools.R
-1d324dce1bbb0900483dee3c081c4197 *R/navGraph.R
+f0ec55cb22b91af3918f70c881e7bac1 *R/navGraph.R
 e2046071e11a654375f749ae3f73a299 *R/ng_data.R
 341f0517b37a67c8a4f3a8f23e910459 *R/ng_graph.R
 b329d41fa64771577a44a16fadf604a7 *R/ng_image.R
 a99f1c3a3c7c5bab62790b432ad4e06c *R/ng_path.R
 2df6ec796522c5881afa798e4091d435 *R/scagNav.R
-59e83261e9e85cde03449fcdb1f6e190 *R/zzz.R
+f0faaa3bcbd4ac6b9f5be64be8f5326f *R/zzz.R
 05fa39a7aa4a291f0106a0d5c0f1af5f *data/olive.rda
-8e3052319f6b637047d582b58e563930 *demo/00Index
+4c65ddaaa2d9011f2f2ecf1ced77cc38 *demo/00Index
 f6bed440461ba5b5119b13ea84486afe *demo/ng_2d_image_files_aloi.R
 e32ad4ffe3e274a54bf0120920479a26 *demo/ng_2d_images_alpha_letter.R
 f4b98a0bd069bbf827c78a1f221b4c1b *demo/ng_2d_images_digits.R
@@ -35,47 +35,19 @@ e6195073c4c1053f62f75299ab46dc34 *demo/ng_2d_myplot_grid.R
 89f25eb6eaf0221bbc0bd3428111583d *demo/ng_2d_myplot_rgl.R
 19090a35be406de6dc437fef90388679 *demo/ng_2d_olive.R
 893374fbe4c8212a0239feb08c2cdaaa *demo/ng_2d_scagnostics_olive.R
-565ba3355ffdd2649490f106a444f7e1 *inst/doc/RnavGraph.Rnw
-c0fc7fb9522e1aa12c513d40c28e87c4 *inst/doc/RnavGraph.pdf
-878bc5d97e8fc74bcd1c30ecfee54ac4 *inst/doc/img/Iris2D.png
-477b04aa2ae7bae02581a52b705518f3 *inst/doc/img/Iris3Dgraph.png
-cd30f1a534564bf00f5c4cf266f8ec7b *inst/doc/img/all.png
-009b8efae8b69597b198849bfcb93554 *inst/doc/img/aloi.jpg
-6550c8c81e544a37def56fb9a323f2c7 *inst/doc/img/f1_1.png
-1f7ed692604c2607304d03894150b02f *inst/doc/img/f1_2.png
-6c7a5413dc5235a93d922c01c3d41a80 *inst/doc/img/f2_1.png
-46ea8aa7c6fd8690a6e4825577fae793 *inst/doc/img/f2_2.png
-22d80a8c8cfc0cb0415ef8c8ec64ff9e *inst/doc/img/ggobicolors.png
-e85e39f0c1b31174122301a7ebf530dd *inst/doc/img/graph.eps
-65578f85a79af4fee98a76464e1328ab *inst/doc/img/graph.png
-b1e6188270d3e23696fa39eb03f83d93 *inst/doc/img/imageDigits.png
-25c8907faab1358cdd0009ddd7141303 *inst/doc/img/m1_1.png
-0a1e7bdc76999567e86815d11dbe081b *inst/doc/img/m1_2.png
-7343d5059fdf3a0b7f10bf6d08ef2fc0 *inst/doc/img/m2_1.png
-401e400fdc0dbdc1bfbfb372df2f13c6 *inst/doc/img/m3_1.png
-4593ccbe6481fce1ac3f88a656b723a8 *inst/doc/img/m4_1.png
-1ee7ea1c187f556aa4f5cb25c6476bb7 *inst/doc/img/m4_2.png
-fc413f742ddf8b23403a83ace580cf23 *inst/doc/img/tk2dGlyphs.png
-e013f0b9593f0719daaa6f1d4021b8e4 *inst/doc/img/tk2dImagesObject.png
-d375579ac402230f63022b6c4c175d84 *inst/doc/img/tk2dcolors.png
-da4df93cb36f339047580637e3cb2e03 *inst/doc/img/tk2dcolors2.png
-e779e463f7a934c1bdb9915ec1fe86c7 *inst/doc/img/tk2dimages1.png
-43fad6779d744553274c9bf95c1833c8 *inst/doc/lg.tex
-e13b04983886f49dac831bda2cba3aa2 *inst/doc/p_prod.tex
-dd48da26f924e1d4d2653d3105578d84 *inst/doc/products.tex
-4b6a83fceb0a46bd44a28412e738589e *inst/doc/rep_p_GLG.tex
-dc58885a2f671bc0d1584f82463777cd *inst/doc/temp.tex
-2c834ba48bb44cb8c139d56a17c6a8c4 *inst/doc/tikz_animation.tex
-aafd56543b925aed202d49f92d882273 *inst/doc/tikz_drag.tex
-cc550adbced477dcddcbea1f5437a6b9 *inst/doc/tikz_edgeSelect.tex
-3b3f4674b263a815e75f0e6a66d18852 *inst/doc/tikz_modifyGraph.tex
-28d4af98c9a46f85b9261de3ca6029ea *inst/doc/tikz_tk2d_main.tex
-d0c5c9a08c6b1dcb3ac39801d14d9a44 *inst/doc/tikz_walk.tex
+ff1cda694de51a83619676e3aca1c099 *demo/ng_own_viz.R
+0a75373364cfcf4acae0aa67e48c3533 *inst/doc/RnavGraph.Rnw
+e084b049d0c279a64fb3879ebc2d99a2 *inst/doc/RnavGraph.pdf
 b32561c5cecdc451ee9a893f3efecd4b *inst/tcl/GraphDisplay.tcl
 ffbe67dcab0a0c7cf371524ffcba5a4d *inst/tcl/tkScatterplotV1.tcl
 94bfc13ab09e12cfb4bbc2b23e0f4c05 *inst/tcl/tkScatterplotV3.tcl
+7fe06be4cd19b953d792103066d4f82d *man/NG_Visualization-class.Rd
 fcf942d65d03b25a11106409c14af668 *man/RnavGraph-package.Rd
+07922988b115e438a8e5add4336c8c4f *man/closeViz-methods.Rd
+700a1961452feac558f03008d4472a0d *man/closeViz.Rd
 16a162c79bcfcde2903c1a68051cf96b *man/completegraph.Rd
+7d1c17f72800605005eeb066e8d6a350 *man/initializeViz-methods.Rd
+097a6a3720a0d3ee8d81ff1f9dde583f *man/initializeViz.Rd
 fec7fc31e3554fea6c084b41c91277a6 *man/linegraph-methods.Rd
 e12bacf23993c4833cf2f18e24fa523f *man/linegraph.Rd
 23fc1cc5fa7dc02e4cba238cf144d005 *man/names-methods.Rd
@@ -97,10 +69,10 @@ c4adb6b9a195636bd632ac7d9f98ffa2 *man/ng_set-methods.Rd
 20eca46584cd0f5fdd3fa813afc74eff *man/ng_set.Rd
 a18077f974df647145afbc7b7be162ff *man/ng_set_--methods.Rd
 5a778a47bffaa80d1b14abb1dc81837f *man/ng_set_color_--methods.Rd
-e7f2e37780f69804800bf24df4f60407 *man/ng_set_colorsetter.Rd
+2c796181da603415f70c15cb68840ed6 *man/ng_set_colorsetter.Rd
 eb5cc7203ef6e31da1ac058b6be5f405 *man/ng_set_size_--methods.Rd
-54a4889c51d158d2e449b2c2d6b8d972 *man/ng_set_sizesetter.Rd
-41cf0b2979793d8723fbf6327e3fd8d0 *man/ng_setsetter.Rd
+dab227fdd3ebe78b0019edd970f30e73 *man/ng_set_sizesetter.Rd
+d4adcce739a2d0ea40775f6decaa9306 *man/ng_setsetter.Rd
 fd830993143b83dc528b652468fb0ef3 *man/ng_update.Rd
 bdf78bafb92240d4cc24ff5bbf26ebe0 *man/ng_walk.Rd
 28ccdf988d3266fda946af0b3194b1ce *man/olive.Rd
@@ -112,6 +84,44 @@ af1140459efe391285be1eff17bb98d0 *man/scagGraph.Rd
 13495c077cf5f60c74ce6338a5c7b500 *man/shortnames.Rd
 4f10aaa642791491f9f5682292a5bc22 *man/shortnames_--methods.Rd
 1527379a32776e5ad9114d4eaa2ebb60 *man/shortnamessetter.Rd
+a233838b132c5818970c6e4843fc94b3 *man/updateViz-methods.Rd
+21695414dce36a7a74d23d503d92d3a5 *man/updateViz.Rd
 fed9c5a7460a05800eabd118db8fc5f3 *src/Makevars
-5a0116afd444d3d14245405f57f6f379 *src/display_stuff.c
+29e0eb8662afe7e7b664ba8120fd9867 *src/display_stuff.c
 c6976d3548df7b5c048cdb5924166d8f *src/image_scale.c
+0a75373364cfcf4acae0aa67e48c3533 *vignettes/RnavGraph.Rnw
+878bc5d97e8fc74bcd1c30ecfee54ac4 *vignettes/img/Iris2D.png
+477b04aa2ae7bae02581a52b705518f3 *vignettes/img/Iris3Dgraph.png
+cd30f1a534564bf00f5c4cf266f8ec7b *vignettes/img/all.png
+009b8efae8b69597b198849bfcb93554 *vignettes/img/aloi.jpg
+6550c8c81e544a37def56fb9a323f2c7 *vignettes/img/f1_1.png
+1f7ed692604c2607304d03894150b02f *vignettes/img/f1_2.png
+6c7a5413dc5235a93d922c01c3d41a80 *vignettes/img/f2_1.png
+46ea8aa7c6fd8690a6e4825577fae793 *vignettes/img/f2_2.png
+22d80a8c8cfc0cb0415ef8c8ec64ff9e *vignettes/img/ggobicolors.png
+e85e39f0c1b31174122301a7ebf530dd *vignettes/img/graph.eps
+65578f85a79af4fee98a76464e1328ab *vignettes/img/graph.png
+b1e6188270d3e23696fa39eb03f83d93 *vignettes/img/imageDigits.png
+25c8907faab1358cdd0009ddd7141303 *vignettes/img/m1_1.png
+0a1e7bdc76999567e86815d11dbe081b *vignettes/img/m1_2.png
+7343d5059fdf3a0b7f10bf6d08ef2fc0 *vignettes/img/m2_1.png
+401e400fdc0dbdc1bfbfb372df2f13c6 *vignettes/img/m3_1.png
+4593ccbe6481fce1ac3f88a656b723a8 *vignettes/img/m4_1.png
+1ee7ea1c187f556aa4f5cb25c6476bb7 *vignettes/img/m4_2.png
+34f2d8d63c5a0b0d766c01cdefc09d08 *vignettes/img/settings.png
+fc413f742ddf8b23403a83ace580cf23 *vignettes/img/tk2dGlyphs.png
+e013f0b9593f0719daaa6f1d4021b8e4 *vignettes/img/tk2dImagesObject.png
+d375579ac402230f63022b6c4c175d84 *vignettes/img/tk2dcolors.png
+da4df93cb36f339047580637e3cb2e03 *vignettes/img/tk2dcolors2.png
+e779e463f7a934c1bdb9915ec1fe86c7 *vignettes/img/tk2dimages1.png
+43fad6779d744553274c9bf95c1833c8 *vignettes/lg.tex
+e13b04983886f49dac831bda2cba3aa2 *vignettes/p_prod.tex
+dd48da26f924e1d4d2653d3105578d84 *vignettes/products.tex
+4b6a83fceb0a46bd44a28412e738589e *vignettes/rep_p_GLG.tex
+dc58885a2f671bc0d1584f82463777cd *vignettes/temp.tex
+2c834ba48bb44cb8c139d56a17c6a8c4 *vignettes/tikz_animation.tex
+aafd56543b925aed202d49f92d882273 *vignettes/tikz_drag.tex
+cc550adbced477dcddcbea1f5437a6b9 *vignettes/tikz_edgeSelect.tex
+3b3f4674b263a815e75f0e6a66d18852 *vignettes/tikz_modifyGraph.tex
+28d4af98c9a46f85b9261de3ca6029ea *vignettes/tikz_tk2d_main.tex
+d0c5c9a08c6b1dcb3ac39801d14d9a44 *vignettes/tikz_walk.tex

NAMESPACE

@@ -24,8 +24,8 @@ importFrom(RBGL,kamadaKawaiSpringLayout,fruchtermanReingoldForceDirectedLayout)
 		scagGraph,
 		scagEdgeWeights,
 		plot,
-               ng_get_color,
-               ng_get_size
+                ng_get_color,
+                ng_get_size
 	)
 #exportPattern("^ng_")
 
@@ -39,7 +39,8 @@ export("ng_set_size<-")
 #export(plot)
 ##visualization
 #exportClass(NG_Visualization, NG_Viz2DAxis)
-#export(inititializeViz, updateViz, closeViz)
+exportClass(NG_Visualization)
+export(initializeViz, updateViz, closeViz)
 ## scagGraph
 #export(scagNav,scagGraph,scagEdgeWeights)
 

NEWS

@@ -1,8 +1,11 @@
+New to Version 0.1.2
+--------------------
+* Added Slicing
+
 New to Version 0.1.1
 --------------------
 * Brushing Bug Fix for tk2d
 
-
 New to Version 0.1.0
 --------------------
 * new functions/methods: ng_get_color, ng_set_color<-, ng_get_size, ng_set_size<-

R/AllGenerics.R

@@ -53,8 +53,8 @@ setGeneric(name = "adjacent",
 
 ## NG_Visualization
 setGeneric(
-		name = "inititializeViz",
-		def = function(viz,ngEnv){standardGeneric("inititializeViz")})
+		name = "initializeViz",
+		def = function(viz,ngEnv){standardGeneric("initializeViz")})
 
 setGeneric(
 		name = "updateViz",

R/FunctionNavGraph.R

@@ -27,7 +27,7 @@
 ## switching a graph calls .closePlots and .initializePlots
 ## changing the bullet state invokes .updatePlots
 .initializePlots <- function(ngEnv) {
-	assign(ngEnv$selViz,sapply(get(ngEnv$selViz,envir = ngEnv),function(viz)inititializeViz(viz,ngEnv)),envir = ngEnv)	
+	assign(ngEnv$selViz,sapply(get(ngEnv$selViz,envir = ngEnv),function(viz)initializeViz(viz,ngEnv)),envir = ngEnv)	
 }
 
 .updatePlots <- function(ngEnv) {

R/Visualization2D.R

@@ -233,3 +233,6 @@ ng_2d_dist <- function(viz,ngEnv) {
 	}
 	return(d)
 }
+
+
+

R/Viz2D_Axis.R

@@ -45,7 +45,7 @@ ng_2d_myplot <- function(data,graph,fnName, device = "base", scaled=TRUE){
 
 
 setMethod(
-		f = "inititializeViz",
+		f = "initializeViz",
 		signature = "NG_Viz2DAxis",
 		definition = function(viz,ngEnv){
 

R/Viz2D_Ggobi.R

@@ -44,7 +44,7 @@ ng_2d_ggobi <- function(data,graph){
 
 ## Initialize Plots
 setMethod(
-		f = "inititializeViz",
+		f = "initializeViz",
 		signature = "NG_Viz2D_Ggobi",
 		definition = function(viz,ngEnv){
 

R/Viz2D_tk2d.R

@@ -76,7 +76,7 @@ ng_2d <- function(data, graph, images = NULL, glyphs = NULL) {
 
 ## Initialize Plots
 setMethod(
-		f = "inititializeViz",
+		f = "initializeViz",
 		signature = "NG_Viztk2d",
 		definition = function(viz,ngEnv){
 

R/navGraph.R

@@ -58,7 +58,7 @@ navGraph <- function(data, graph = NULL, viz = NULL, settings = NULL) {
 					if(all(sapply(get(arg),function(x){is(x,arg_class)}))){
 						assign(paste(arg,"List", sep = ''),get(arg))	
 					}else{
-						stop(paste("[navGraph] elements in list ",arg," are not from class NG_",arg, sep = ''))
+						stop(paste("[navGraph] elements in list ",arg," are not from class ",arg_class, sep = ''))
 					}
 				} else {
 					stop(paste("[navGraph] argument ",arg," is neither a list of NG_", arg," objects nor a NG_", arg," object",sep = ''))
@@ -927,7 +927,7 @@ navGraph <- function(data, graph = NULL, viz = NULL, settings = NULL) {
 
 
 	## Tk Canvas Scatterplot
-	whichScaledData <- sapply(vizList,function(x){any(class(x) %in% c("NG_Viztk2d","NG_Viz2DAxis"))})
+	whichScaledData <- sapply(vizList,function(x){is(x,"NG_Viztk2d")|is(x,"NG_Viz2DAxis")})
 
 	if(any(whichScaledData)) {
 		ngEnv$scaledData <- list()
@@ -960,7 +960,7 @@ navGraph <- function(data, graph = NULL, viz = NULL, settings = NULL) {
 
 		ngEnv$t.vizcounter <- 1
 		vizList <- lapply(vizList, FUN = function(viz){
-					if(class(viz) == "NG_Viztk2d") {
+					if(is(viz,"NG_Viztk2d")) {
 
 						viz@viz_name <- paste("viz",t.vizcounter,sep = '') 
 						vizN <- viz@viz_name

R/zzz.R

@@ -18,17 +18,15 @@
 	## load Img tk extension
 	sysname <- Sys.info()[1]
 	didLoad <- TRUE
-	if(sysname == "Windows") {
-		## TODO: Img extension for windows. Alternative R functions?
-	} else if (sysname == "Darwin") {
+	if (sysname == "Darwin") {
 		addTclPath("/System/Library/Tcl")
 		didLoad <- tclRequire('Img')
 	} else {
 		didLoad <- tclRequire('Img')
 	}
 
 	if(identical(didLoad,FALSE)) {
-		warning("Can not load the tk Img extension. Hence you can not use the 'ng_image_files' R function.")	
+		warning("Can not load the tk Img extension. Hence you can not use the 'ng_image_files' R function. Read the package vignette on how to set up tcl/tk.")	
 	}
 
 }
@@ -37,4 +35,4 @@
 	packageStartupMessage("\nRnavGraph Version ",
 			utils::packageDescription("RnavGraph", field="Version"),
 			'\nPlease read the package vignette. Use vignette("RnavGraph").\n\n')	
-}
+}

demo/00Index

@@ -12,3 +12,4 @@ ng_2d_myplot_grid	Scatterplots using the grid plotting device, data = iris
 ng_2d_myplot_rgl	Scatterplots using the rgl plotting device, data = iris
 ng_2d_myplot_hexbin	Bivariate Binning into Hexagon Cells, data = iris
 ng_2d_scagnostics_olive	Scagnostics example using the olive data set
+ng_own_viz	Create own visualization instructions using initializeViz, updateViz and closeViz