mcaGUI
Microbial Community Analysis GUI

Package index
Search the mcaGUI package
Functions
229
Source code
31
Man pages
5
Home
/
Bioconductor
/
mcaGUI
/
R/menus.R

R/menus.R
In mcaGUI: Microbial Community Analysis GUI

Defines functions handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler handler 

### Define the main menu here

OTUbase.menu=list()
pmg.menu = list()
pmg.menu$File$"Read OTU Base"$handler =
  function(h,...) OTUbasereader()
pmg.menu$File$"Read OTU Base"$icon="file"

pmg.menu$File$"Read Proportion or Count Table"$handler =
  function(h,...) Proportion_Or_Count_Reader()
pmg.menu$File$"Read Proportion or Count Table"$icon="file"

pmg.menu$File$"Read Table"$handler =
 function(h,...) pmg.gw(read.table.list)
pmg.menu$File$"Read Table"$icon="file"


pmg.menu$File$"Save Workspace..."$handler =
  function(h,...) gfile("Save workspace",type="save", action="save.image")
pmg.menu$File$"Save Workspace..."$icon = "save"
pmg.menu$File$"Restore Workspace"$handler =
  function(h, ...) gfile("Restore workspace",type="open", action="load")
pmg.menu$File$"Restore Workspace"$icon = "revert-to-saved"
pmg.menu$File$"Load package..."$handler =
  function(h,...) pmg.loadPackages()
pmg.menu$File$"Install CRAN package..."$handler =
  function(h,...) pmg.installCRANPackage()
pmg.menu$File$"Install CRAN package..."$icon = "network"
pmg.menu$File$"Install local package..."$handler =
  function(h,...) {
    old = options("repos")$repos; options("repos"=NULL);
    gfile("Select a package file...","open",action="install.packages",
          filter=   list(
            "tar.gz files"=list(
              patterns=c("*.tgz","*.tar.gz")
              ),
            "zip files"=list(
              patterns=c("*.zip")
              ),
            "All files"=list(
              patterns=c("*")
              )
            )
          )
    options("repos"=old)
  }
pmg.menu$File$"Install local package..."$icon = "file"
pmg.menu$File$"Set working directory..."$handler =
  function(h,...) gfile("Select a directory","selectdir",action="setwd")
pmg.menu$File$"Set working directory..."$icon = "directory"


pmg.menu$File$"View window list"$handler = function(h,...) pmgWC$show()
pmg.menu$File$"Exit mcaGUI"$handler =
  function(h,...)  {
    dispose(pmg.dialogs.window)
    assignInNamespace("pmg.dialogs.window", NULL,"mcaGUI")
    pmg.closeAll()
  }
pmg.menu$File$"Exit mcaGUI"$icon ="quit"
##
##
pmg.menu$Data$browseEnv$handler =
  function(h,...) browseEnv()
pmg.menu$Data$"Load data set..."$handler =
  function(h,...) pmg.viewDataSets()
pmg.menu$Data$"Import data set..."$handler =
  function(h,...) pmg.specifyFileForImport();
pmg.menu$Data$"Write data as CSV file..."$handler =
  function(h,...) pmg.gw(write.csv.list)
pmg.menu$Data$"Abundance Table"$handler =
  function(h,...) {
  g1 = ggroup(use.scrollwindow=TRUE)
  add(pmg.dialog.notebook, g1, label="Abundance Table", pageno = 3)

  tbl <- glayout(cont=g1, expand=FALSE)

  tbl[1,1] = (glabel(text="object", containter=tbl))
  tbl[1,2] = (object <- gedit(text ="", container=tbl))
  tbl[1,3] = (glabel(text="weighted", container=tbl))
  tbl[1,4] = (weight <- gradio(items=c("TRUE", "FALSE"), container=tbl))

  tbl[2,1] = (glabel(text="Sample data as rows?"))
  tbl[2,2] = (transpose <- gradio(items=c("No", "Yes"), container=tbl))

  tbl[3,1]= (glabel(text="Assign To", container=tbl))
  tbl[3,2] = (assignTo <- gedit(text="", container=tbl))


  tbl[4,1]= (advanced <- gbutton(text="Update Feature and Sample Meta-Data", container=tbl))

  getUpdate <- function(h,...) {
  assignmentName = paste(svalue(object), "_assignmentData", sep="")
  assignmentName = names(eval(as.symbol(assignmentName)))

  sampleName = paste(svalue(object), "_sampleData", sep="")
  sampleName = names(eval(as.symbol(sampleName)))

  tbl[5,1] = (glabel(text="Feature Data Column", container=tbl))
  tbl[5,2] = (assignmentCol <<- gdroplist(items=assignmentName, container=tbl))
  tbl[6,1] = (glabel(text="Sample Meta-Data Column", container=tbl))
  tbl[6,2] = (collab <<- gdroplist(items=sampleName, container=tbl))
  }

  addHandlerClicked(advanced, handler = getUpdate, action= NULL)

  tbl[7,1] = (createAbundance <- gbutton(text="Create Abundance Table", container=tbl))

  createAbundanceTable <- function(h,...) {
    checkAssignment = mget("assignmentCol", envir=.GlobalEnv, mode = "any", ifnotfound = list(NA), inherits = FALSE)

    if(is.na(as.list(checkAssignment[1]))) {
      assign(as.character(svalue(assignTo)), abundance(object=eval(as.symbol(svalue(object))), weighted=svalue(weight), envir = .GlobalEnv))
      } else {
      assign(as.character(svalue(assignTo)), abundance(object=eval(as.symbol(svalue(object))), weighted=svalue(weight), assignmentCol=svalue(assignmentCol), collab = svalue(collab)), envir = .GlobalEnv)
    }

    if(svalue(transpose) == "No") {
      assign(as.character(as.symbol(svalue(assignTo))), eval(as.symbol(svalue(assignTo))), envir = .GlobalEnv)
      #rm(list=c("collab","assignmentCol"), envir = .GlobalEnv)
      } else {
      assign(as.character(as.symbol(svalue(assignTo))), t(eval(as.symbol(svalue(assignTo)))), envir = .GlobalEnv)
    }
  }

  addHandlerClicked(createAbundance, handler = createAbundanceTable, action= NULL)
  }
pmg.menu$Data$"Abundance Table"$icon=""              
## dynamic

pmg.menu$Data$"Dynamic summaries"$handler =
  function(h,...) dSummaryDialog()
pmg.menu$Data$"Dynamic summaries"$icon = "execute"
pmg.menu$Data$"Univariate summaries"$table$handler =
  function(h,...) pmg.gw(table.list)
pmg.menu$Data$"Univariate summaries"$"stem and leaf"$handler =
  function(h,...) pmg.gw(stem.list)
pmg.menu$Data$"Univariate summaries"$"summary"$handler =
  function(h,...) pmg.gw(summary.list)
pmg.menu$Data$"Univariate summaries"$"summary"$icon = "info"
pmg.menu$Data$"Univariate summaries"$mean$handler =
  function(h,...) pmg.gw(mean.list)
pmg.menu$Data$"Univariate summaries"$median$handler =
  function(h,...) pmg.gw(median.list)
pmg.menu$Data$"Univariate summaries"$"standard deviation"$handler =
  function(h,...) pmg.gw(sd.list)
pmg.menu$Data$"Univariate summaries"$IQR$handler =
  function(h,...) pmg.gw(IQR.list)
pmg.menu$Data$"Univariate summaries"$mad$handler =
  function(h,...) pmg.gw(mad.list)
pmg.menu$Data$"Univariate summaries"$quantiles$handler =
  function(h,...) pmg.add(quantileWidget(),label="quantile()") # add here
pmg.menu$Data$"Univariate summaries"$skewness$handler =
  function(h,...) pmg.gw(skewnessList)
pmg.menu$Data$"Univariate summaries"$kurtosis$handler =
  function(h,...) pmg.gw(kurtosisList)
##
pmg.menu$Data$"Bivariate summaries"$correlation$handler =
  function(h,...) pmg.gw(cor.list)
pmg.menu$Data$"Bivariate summaries"$"Cross tabulation"$handler =
  function(h,...) pmg.gw(xtabs.list)
##
pmg.menu$Data$"Nonparametric Bootstrap Summaries"$handler =
  function(h,...) pmg.gw(bootstrap.list)
##
pmg.menu$Data$"Random data"$"Cumulative Probabilities"$handler = function(h,...) 
  add(pmg.dialog.notebook,dpqrfuncs(type="p"),label="p funcs")
pmg.menu$Data$"Random data"$"Probabilities"$handler = function(h,...) 
  add(pmg.dialog.notebook,dpqrfuncs(type="d"),label="d funcs")
pmg.menu$Data$"Random data"$Quantiles$handler = function(h,...) 
  add(pmg.dialog.notebook,dpqrfuncs(type="q"),label="q funcs")
pmg.menu$Data$"Random data"$"Random samples"$handler = function(h,...) 
  add(pmg.dialog.notebook,dpqrfuncs(type="r"),label="r funcs")


pmg.menu$Data$"Random data"$"Sample"$handler =
  function(h,...) pmg.gw(sample.list)
##

##########
## Simulation. What else?
pmg.menu$Data$Simulation$"Repeat trials"$handler = function(h,...) {
  add(pmg.dialog.notebook, repeatTrialsGUI(), label = "Repeat trials")
}




## Manipulate
if("reshape" %in% .packages(TRUE)) {
  pmg.menu$Data$"Manipulate"$reshape$melt$handler = function(h,...) pmg.meltGUI()
  pmg.menu$Data$"Manipulate"$reshape$cast$handler = function(h,...) pmg.castGUI()
}


pmg.menu$Data$"Manipulate"$"subset"$handler =
  function(h,...) add(pmg.dialog.notebook,pmg.subset.dialog(),label="subset()")
pmg.menu$Data$"Manipulate"$"subset"$icon = "subset"
pmg.menu$Data$"Manipulate"$"subset"$handler =
  function(h,...) add(pmg.dialog.notebook,pmg.subset.dialog(),label="subset()")
pmg.menu$Data$"Manipulate"$"stack"$handler =
  function(h,...) pmg.gw(stack.list)
pmg.menu$Data$"Manipulate"$"unstack"$handler =
  function(h,...) pmg.gw(unstack.list)
pmg.menu$Data$"Manipulate"$"Edit data frame properties"$handler =
  function(h,...) add(pmg.dialog.notebook,pmg.edit.dataframe.properties.dialog(),label="edit properties")
pmg.menu$Data$"Manipulate"$"Edit data frame properties"$icon = "properties"
##
pmg.menu$Data$"Coerce"$"as.numeric"$handler =
  function(h,...) pmg.gw(as.numeric.list)
pmg.menu$Data$"Coerce"$"as.character"$handler =
  function(h,...) pmg.gw(as.character.list)
pmg.menu$Data$"Coerce"$"as.data.frame"$handler =
  function(h,...) pmg.gw(as.data.frame.list)
pmg.menu$Data$"Coerce"$"as.matrix"$handler =
  function(h,...) pmg.gw(as.matrix.list)
pmg.menu$Data$"Coerce"$"matrix"$handler =
  function(h,...) pmg.gw(matrix.list)
pmg.menu$Data$"Coerce"$"groupedData"$handler =
  function(h,...) pmg.gw(groupedData.list)
pmg.menu$Data$"Coerce"$"factor"$handler =
  function(h,...) pmg.gw(factor.list)
##
## Plots
## Dynamic widget
pmg.menu$Plots$"Lattice explorer"$handler = function(h,...) {
  dLatticeExplorer(container=pmgWC$new("Lattice explorer", v=T))
}
pmg.menu$Plots$"Lattice explorer"$icon = "execute"
###
pmg.menu$Plots$"Set plot parameters"$Setup$handler =
  function(h,...) pmg.gw(par.setup.list)
pmg.menu$Plots$"Set plot parameters"$Setup$icon = "preferences"
pmg.menu$Plots$"Set plot parameters"$Axes$handler =
  function(h,...) pmg.gw(par.axes.list)
pmg.menu$Plots$"Set plot parameters"$Axes$icon = "preferences"
pmg.menu$Plots$"Set plot parameters"$Colors$handler =
  function(h,...) pmg.gw(par.colors.list)
pmg.menu$Plots$"Set plot parameters"$Colors$icon = "preferences"
pmg.menu$Plots$"Set plot parameters"$Fonts$handler =
  function(h,...) pmg.gw(par.fonts.list)
pmg.menu$Plots$"Set plot parameters"$Fonts$icon = "preferences"
pmg.menu$Plots$"Set plot parameters"$"Number of figures"$handler =
  function(h,...) pmg.gw(par.nofigures.list)
pmg.menu$Plots$"Set plot parameters"$"Number of figures"$icon = "preferences"

##
pmg.menu$Plots$univariate$"barplot"$handler = 
  function(h,...) pmg.gw(barplot.list)
pmg.menu$Plots$univariate$"barplot"$icon="barplot"
pmg.menu$Plots$univariate$"piechart"$handler = 
  function(h,...) pmg.gw(piechart.list)
pmg.menu$Plots$univariate$"boxplot"$handler = 
  function(h,...) pmg.gw(univariate.boxplot.list)
pmg.menu$Plots$univariate$"boxplot"$icon = "boxplot"
pmg.menu$Plots$univariate$"histogram"$handler = 
  function(h,...) pmg.gw(hist.list)
pmg.menu$Plots$univariate$"histogram"$icon ="hist"
pmg.menu$Plots$univariate$"density plot"$handler = 
  function(h,...) pmg.gw(densityplot.list)
pmg.menu$Plots$univariate$"quantile-normal plot"$handler = 
  function(h,...) pmg.gw(qqnorm.list)
pmg.menu$Plots$univariate$"stripchart"$handler = 
  function(h,...) pmg.gw(stripchart.list)
pmg.menu$Plots$univariate$"dotchart"$handler = 
  function(h,...) pmg.gw(dotchart.list)
pmg.menu$Plots$univariate$"ecdf"$handler = 
  function(h,...) pmg.gw(ecdf.list)
##
pmg.menu$Plots$bivariate$"boxplot"$handler = 
  function(h,...) pmg.gw(bivariate.boxplot.list)
pmg.menu$Plots$bivariate$"boxplot"$icon = "boxplot"
pmg.menu$Plots$bivariate$"scatterplot"$handler = 
  function(h,...) pmg.gw(scatterplot.list)
pmg.menu$Plots$bivariate$"scatterplot"$icon = "points"
pmg.menu$Plots$bivariate$"sunflower plot"$handler = 
  function(h,...) pmg.gw(sunflower.list)
pmg.menu$Plots$bivariate$"quantile-quantile plot"$handler = 
  function(h,...) pmg.gw(qqplot.list)
##
pmg.menu$Plots$multivariate$"plot"$handler = 
  function(h,...) pmg.gw(scatterplot.model.list)
pmg.menu$Plots$multivariate$"plot"$icon = "plot"
pmg.menu$Plots$multivariate$"boxplot"$handler = 
  function(h,...) pmg.gw(model.boxplot.list)
pmg.menu$Plots$multivariate$"boxplot"$icon = "boxplot"
pmg.menu$Plots$multivariate$"pairs plot"$handler = 
  function(h,...) pmg.gw(pairs.list)
##
pmg.menu$Plots$"Lattice graphics"$"xyplot"$handler = 
  function(h,...) pmg.gw(xyplot.list)
pmg.menu$Plots$"Lattice graphics"$"dotplot"$handler = 
  function(h,...) pmg.gw(dotplot.list)
pmg.menu$Plots$"Lattice graphics"$"barchart"$handler = 
  function(h,...) pmg.gw(barchart.list)
pmg.menu$Plots$"Lattice graphics"$"stripplot"$handler = 
  function(h,...) pmg.gw(stripplot.list)
pmg.menu$Plots$"Lattice graphics"$"bwplot"$handler = 
  function(h,...) pmg.gw(bwplot.list)
##
pmg.menu$Plots$"Add to graphic"$"points"$handler = 
  function(h,...) pmg.gw(add.points.list)
pmg.menu$Plots$"Add to graphic"$"points"$icon = "points"
pmg.menu$Plots$"Add to graphic"$"lines"$handler = 
  function(h,...) pmg.gw(add.lines.list)
pmg.menu$Plots$"Add to graphic"$"lines"$icon = "lines"
pmg.menu$Plots$"Add to graphic"$"density"$handler = 
  function(h,...) pmg.gw(add.density.list)
pmg.menu$Plots$"Add to graphic"$"curve"$handler = 
  function(h,...) pmg.gw(add.curve.list)
pmg.menu$Plots$"Add to graphic"$"curve"$icon = "curve"
pmg.menu$Plots$"Add to graphic"$"rug"$handler = 
  function(h,...) pmg.gw(rug.list)
pmg.menu$Plots$"Add to graphic"$"title"$handler = 
  function(h,...) pmg.gw(add.title.list)


## iplots conditionally
if("iplots" %in% .packages(TRUE)) {
  pmg.menu$Plots$"iplots"$handler = function(...) {
    pmg.iplots()
  }
}


help.menu=list()
help.menu$Help$"About R"$handler =
  function(h,...) add(pmg.dialog.notebook,pmg.about.R(),label = "About R")
#help.menu$Help$"About PMG"$handler =
  function(h,...) add(pmg.dialog.notebook,pmg.about(),label = "About P M G")
##pmg.about(container=pmgWC$new(v=TRUE))
#help.menu$Help$"About PMG"$icon="about"
help.menu$Help$"R helpbrowser"$handler =
  function(h,...) {
    if(is.null(pmg.helpBrowser.window) ||
       is.invalid(pmg.helpBrowser.window)) {
      assignInNamespace("pmg.helpBrowser.window", ghelpbrowser(),"mcaGUI")
    } else {
      focus(pmg.helpBrowser.window) <- TRUE # will this work
    }
  }
help.menu$Help$"View mcaGUI vignette"$handler = function(h,...) browseURL(system.file("doc","An_Introduction_and_User_Guide_for_mcaGUI.pdf",package="mcaGUI"))
#help.menu$Help$"R Site Search"$handler = function(h,...) RSiteSearch.Dialog()
#help.menu$Help$"View vignettes"$handler = function(h,...) viewVignettes.Dialog()
#help.menu$Help$"View demos"$handler = function(h,...) viewDemos.Dialog()
#help.menu$Help$"View P M G vignette"$handler = function(h,...) print(vignette("pmg",package="pmg"))

pmg.menu$Analysis$"Richness Estimation"$handler =
  function(h,...) pmg.gw(richness.list)
pmg.menu$Analysis$"Richness Estimation"$icon=""
pmg.menu$Analysis$"Diversity Estimation"$handler =
  function(h,...) pmg.gw(diversity.list)
pmg.menu$Analysis$"Diversity Estimation"$icon=""
pmg.menu$Analysis$"Multivariate"$"Cluster Analysis"$handler =
  function(h,...) pmg.gw(cluster.list)
pmg.menu$Analysis$"Multivariate"$"Cluster Analysis"$icon=""

pmg.menu$Analysis$"Multivariate"$"Principle Component Analysis (PCA)"$handler =
  function(h,...) pmg.gw(prcomp.list )
pmg.menu$Analysis$"Multivariate"$"Principle Component Analysis (PCA)"$icon=""

Try the mcaGUI package in your browser

Any scripts or data that you put into this service are public.

mcaGUI documentation built on Nov. 8, 2020, 7:52 p.m.

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close