RcmdrPlugin.BiclustGUI.Extra: Title: 'Rcmdr' Plug-in GUI for Biclustering

A plug-in for R Commander ('Rcmdr'). The package is a Graphical User Interface (GUI) in which several biclustering methods can be executed, followed by diagnostics and plots of the results. Further, the GUI also has the possibility to connect the methods to more general diagnostic packages for biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG', 'isa2', 'BiBitR', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and 'BcDiag' are also implemented to be able to further investigate results. The GUI also provides a couple of extra utilities to export, save, search through and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific framework for biclustering in which new methods, diagnostics and plots can be added. Scripts were prepared so that R-package developers can freely design their own dialogs in the GUI which can then be added by the maintainer of 'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk' and 'Rcmdr' and are easy to fill in.

AuthorDe Troyer Ewoud, Otava Martin
Date of publication2017-01-24 15:33:45
MaintainerDe Troyer Ewoud <ewoud.detroyer@uhasselt.be>
LicenseGPL-3 + file LICENSE
Version1.1.0

View on R-Forge

Functions

.add.frame Man page
as.ExprSet Man page
.AssignEnvBiclustGUI Man page
bcdiaghighlight_WINDOW Man page
BCDIAG_isa2biclust Man page
bcdiag_WINDOW Man page
bcdiagwrite_WINDOW Man page
bibit3_BC_GUI Man page
bibit3_WIN Man page
bibit_WIN Man page
.bicare2biclust Man page
bicarebiclust_WINDOW Man page
bicare.genesetenrichment Man page
bicare.GUI Man page
bicare.makereport Man page
bicare.pdata Man page
bicare.residuplot Man page
bicare.samplesenrichment Man page
bicare_WINDOW Man page
biclust.bimax.GUI Man page
biclustbimax_WIN Man page
biclustCC_WIN Man page
biclustextraplots_WINDOW Man page
biclustGUI_help Man page
biclustguiwebsitelink Man page
biclustplaid_WIN Man page
biclust.quest.GUI Man page
biclustquest_WIN Man page
biclust.robust.fuse Man page
biclust.robust.fuse.GUI Man page
biclustspectral_WIN Man page
biclustXMotif_WIN Man page
.binary.activematrix.check Man page
.build.button.function Man page
.build.command.argument Man page
.checkplotgridpref Man page
chooseresultsGUI Man page
clearresults_WINDOW Man page
cluster_template Man page
.combine.rows Man page
.correctdataforresults Man page
.eval.command Man page
export.Biclust Man page
export.fabia Man page
export.fabia.threshL Man page
exportFURBY_WINDOW Man page
exportTXT_WINDOW Man page
ExtractBiclustersGUI Man page
ExtractBiclustersGUI_general Man page
extractbicluster_WINDOW Man page
.fabia2biclust Man page
fabiabiclust_WINDOW Man page
fabia.biplot Man page
fabialaplace_WIN Man page
fabiapostprojection_WIN Man page
fabiasparsenessprojection_WIN Man page
fabiaSPARSE_WIN Man page
FindBiclusters Man page
findbiclusters_WINDOW Man page
.find.frame Man page
.GetEnvBiclustGUI Man page
.give.doublequote Man page
greenred Man page
.grid.matrix Man page
HeatmapBC.GUI Man page
iBBiG_WIN Man page
image_WINDOW Man page
indexedBic Man page
.initialize.grid.config Man page
.initialize.grid.rows Man page
.initialize.new.frames Man page
.isa2biclust Man page
isadefault_WIN Man page
isa.extract Man page
isaextraplots_WINDOW Man page
isa.GUI Man page
isa.scoreplots Man page
isa.summary Man page
.isbiclustGUIresult Man page
.isBiclustresult Man page
.is.binary.matrix Man page
.isISA Man page
.isListofBiclustGUIresults Man page
jaccard_WINDOW Man page
.make.correct.frame Man page
.makeResultList Man page
.makesearchdata Man page
.makeSuperbiclustResultList Man page
MaxBC_WINDOW Man page
newmethod_WINDOW Man page
newtool_template Man page
newtool_WINDOW Man page
openGUIScripts Man page
openGUIVignette Man page
.order.button.frames Man page
.output.sparse.txt Man page
parallelCoordinates2 Man page
parallelCoordinates3 Man page
plotgridpref_WINDOW Man page
plotSuper.GUI Man page
.putbefore Man page
RcmdrPlugin.BiclustGUI Man page
RcmdrPlugin.BiclustGUI-package Man page
.rcmdr.warning Man page
redgreen Man page
repeatanalysis.GUI Man page
robust.fuse.support Man page
robust.reset Man page
rqubic.GUI Man page
rqubic_WINDOW Man page
s4vd_WIN Man page
saveload_WINDOW Man page
SearchMethodData Man page
search_WINDOW Man page
Setwd Man page
shinylinkstandalone Man page
shinylinkwebsite Man page
spfabia.GUI Man page
ssvd_WIN Man page
summaryBICARE Man page
superbiclust.GUI Man page
superbiclust.robust.GUI Man page
superbiclust_WINDOW Man page
.tobiclust Man page
.tobiclust_transf Man page
.transform.vector2text Man page
.update.biclustering.object Man page
viridis Man page
writeBic.GUI Man page

Files

RcmdrPlugin.BiclustGUI.Extra/DESCRIPTION
RcmdrPlugin.BiclustGUI.Extra/LICENSE
RcmdrPlugin.BiclustGUI.Extra/NAMESPACE
RcmdrPlugin.BiclustGUI.Extra/NEWS
RcmdrPlugin.BiclustGUI.Extra/R
RcmdrPlugin.BiclustGUI.Extra/R/BicARE_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/BicARE_biclustWIN.R RcmdrPlugin.BiclustGUI.Extra/R/MAINTAINER_functions.R RcmdrPlugin.BiclustGUI.Extra/R/MAINTAINER_transformation_functions.R RcmdrPlugin.BiclustGUI.Extra/R/MaxBC_window.R RcmdrPlugin.BiclustGUI.Extra/R/bcdiag_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/bcdiagwrite_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/bibit3WIN.R RcmdrPlugin.BiclustGUI.Extra/R/bibitWIN.R RcmdrPlugin.BiclustGUI.Extra/R/biclust_extraplotsWIN.R RcmdrPlugin.BiclustGUI.Extra/R/bimaxWIN.R RcmdrPlugin.BiclustGUI.Extra/R/ccWIN.R RcmdrPlugin.BiclustGUI.Extra/R/clearresults_plotgrid_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/exportFURBY_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/exportFURBY_functions.R RcmdrPlugin.BiclustGUI.Extra/R/exportTXT_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/extra_for_biclustGUI.R RcmdrPlugin.BiclustGUI.Extra/R/extract_functions.R RcmdrPlugin.BiclustGUI.Extra/R/extractbicluster_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/fabia_SPARSEWIN.R RcmdrPlugin.BiclustGUI.Extra/R/fabia_biclustWIN.R RcmdrPlugin.BiclustGUI.Extra/R/fabia_laplacepriorWIN.R RcmdrPlugin.BiclustGUI.Extra/R/fabia_postprojectionWIN.R RcmdrPlugin.BiclustGUI.Extra/R/fabia_sparsenessprojectionWIN.R RcmdrPlugin.BiclustGUI.Extra/R/find_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/find_functions.R RcmdrPlugin.BiclustGUI.Extra/R/help_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/iBBiGWIN.R RcmdrPlugin.BiclustGUI.Extra/R/image_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/image_functions.R RcmdrPlugin.BiclustGUI.Extra/R/internal-objectcreating.R RcmdrPlugin.BiclustGUI.Extra/R/internal.R RcmdrPlugin.BiclustGUI.Extra/R/internals_otherpackages.R RcmdrPlugin.BiclustGUI.Extra/R/isa2_defaultWIN.R RcmdrPlugin.BiclustGUI.Extra/R/isa_extraplotsWIN.R RcmdrPlugin.BiclustGUI.Extra/R/jaccardindex_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/justdoit2.R RcmdrPlugin.BiclustGUI.Extra/R/newmethod_function.R RcmdrPlugin.BiclustGUI.Extra/R/newtool_function.R RcmdrPlugin.BiclustGUI.Extra/R/plaidWIN.R RcmdrPlugin.BiclustGUI.Extra/R/questWIN.R RcmdrPlugin.BiclustGUI.Extra/R/rqubic_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/s4vd_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/saveload_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/search_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/spectralWIN.R RcmdrPlugin.BiclustGUI.Extra/R/ssvd_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/superbiclust_WIN.R RcmdrPlugin.BiclustGUI.Extra/R/xmotifWIN.R
RcmdrPlugin.BiclustGUI.Extra/build
RcmdrPlugin.BiclustGUI.Extra/build/vignette.rds
RcmdrPlugin.BiclustGUI.Extra/inst
RcmdrPlugin.BiclustGUI.Extra/inst/doc
RcmdrPlugin.BiclustGUI.Extra/inst/doc/GuideBiclustGUI.Rnw
RcmdrPlugin.BiclustGUI.Extra/inst/doc/GuideBiclustGUI.pdf
RcmdrPlugin.BiclustGUI.Extra/inst/doc/frames_script.R
RcmdrPlugin.BiclustGUI.Extra/inst/doc/installation_script.R
RcmdrPlugin.BiclustGUI.Extra/inst/doc/newmethod_script.R
RcmdrPlugin.BiclustGUI.Extra/inst/doc/newtool_script.R
RcmdrPlugin.BiclustGUI.Extra/inst/etc
RcmdrPlugin.BiclustGUI.Extra/inst/etc/menus.txt
RcmdrPlugin.BiclustGUI.Extra/man
RcmdrPlugin.BiclustGUI.Extra/man/BiclustGUI.Rd RcmdrPlugin.BiclustGUI.Extra/man/GUIfunctions.Rd RcmdrPlugin.BiclustGUI.Extra/man/internals.Rd RcmdrPlugin.BiclustGUI.Extra/man/scriptsinternals.Rd RcmdrPlugin.BiclustGUI.Extra/man/windows.Rd
RcmdrPlugin.BiclustGUI.Extra/vignettes
RcmdrPlugin.BiclustGUI.Extra/vignettes/GuideBiclustGUI-concordance.tex
RcmdrPlugin.BiclustGUI.Extra/vignettes/GuideBiclustGUI.Rnw
RcmdrPlugin.BiclustGUI.Extra/vignettes/GuideBiclustGUI.txt
RcmdrPlugin.BiclustGUI.Extra/vignettes/ThesisBiclustGUIbib.bib
RcmdrPlugin.BiclustGUI.Extra/vignettes/appendix_scripts
RcmdrPlugin.BiclustGUI.Extra/vignettes/appendix_scripts/frames_script.R
RcmdrPlugin.BiclustGUI.Extra/vignettes/appendix_scripts/installation_script.R
RcmdrPlugin.BiclustGUI.Extra/vignettes/appendix_scripts/newmethod_script.R
RcmdrPlugin.BiclustGUI.Extra/vignettes/appendix_scripts/newtool_script.R
RcmdrPlugin.BiclustGUI.Extra/vignettes/appendix_scripts/plaid_script.R
RcmdrPlugin.BiclustGUI.Extra/vignettes/asa.bst
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/MaxBC.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/MaxBC_example.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bcdiag_build.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bcdiag_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bcdiag_example2.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bcdiag_example3.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bcdiag_fabia.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bcdiag_summary.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bibit3_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bibit3_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bibit_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bibit_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicare_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicare_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicare_example2.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicare_example3.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicare_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustGUI_diagram.pdf
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclust_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicluster_structures.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bicluster_types.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustering_helpmenu.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustering_menu.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example2.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example3.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example4.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example5.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example6.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/biclustplot_example7.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/bimax_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/cc_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/checkboxes.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/combinerows_grid.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/discrbin.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/drawheatmaps_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/drawheatmaps_example2.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/drawheatmapswindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/entryfields.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/exportwindows.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/extractwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabia_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabia_sparse.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabialaplace_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiaplot_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiaplot_example2.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiaplot_example3.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiaplot_example4.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiaplot_example5.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiapostproj_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/fabiasparseproj_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/findwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/findwindow_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/ibbig_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/ibbig_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/ibbig_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/isa_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/isa_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/isa_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/jaccardindexwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/logo.jpg
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/manualbutton.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/manualbutton_showsave.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/plaid_clusterbuild.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/plaid_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/plaid_plotdiagbuild.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/plaid_structure.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/plotgridwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/questmotif_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/radiobuttons.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/rcmdr_activedataset.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/rcmdr_datainput.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/rcmdrwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/rqubic_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/rqubic_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/s4vd_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/s4vd_plotdiagtab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/saveloadwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/searchwindow.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/shinyibbig.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/showmethod.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/slider.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/spectral_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/spinboxes.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/ssvd_clusttab.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/standard_buttons.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/superbiclust.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/superbiclust_example1.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/superbiclust_example2.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/title_border.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/window_bottom.png
RcmdrPlugin.BiclustGUI.Extra/vignettes/figures/xmotif_clusttab.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.