Nothing
R/htmlReport.R
In affylmGUI: GUI for limma Package with Affymetrix Microarrays
Defines functions
ExportHTMLreport
GetComponentsToExportInHTMLreport
HTMLplotUsingFunction
Documented in
ExportHTMLreport
GetComponentsToExportInHTMLreport
HTMLplotUsingFunction
HTMLplotUsingFunction <- function(
Caption = "",
File = "plot.html",
GraphRelativeDirectory = ".",
GraphAbsoluteDirectory = NULL,
GraphFileName = "",
GraphSaveAs = "png",
GraphBorder = 1,
Align = "center",
plotFunction = NULL,
Width=600,
Height=600,
PointSize=12,
BG="white",
res=72,
...)
# R2HTML::HTMLplot function modified to accept a plotFunction argument, rather than using the main R Graphics Device.
{
if(is.null(GraphAbsoluteDirectory)){
GraphAbsoluteDirectory <- getwd()
#For eg. "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files"
}
if(GraphFileName == ""){
nowd <- date() #For eg. = "Thu Sep 20 11:27:14 2007"
# 000000000111111111122222
# 123456789012345678901234
GraphFileName <- paste(
"GRAPH_",
substring(nowd, 5, 7),
substring(nowd, 9, 10), "_",
substring(nowd, 12, 13),
substring(nowd, 15, 16),
substring(nowd, 18, 19),
sep = ""
)
# Example name = GRAPH_Sep20_112714
}
GraphFileName <- paste(GraphFileName, GraphSaveAs, sep=".")
# for eg. = GRAPH_Sep20_112714.png
#AbsGraphFileName <- paste(GraphRelativeDirectory,.Platform$file.sep,GraphFileName,sep="")
AbsGraphFileName <- file.path(GraphAbsoluteDirectory, GraphFileName)
#For eg. = "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/GRAPH_Sep20_112714.png"
if(GraphSaveAs=="png"){
if(is.null(plotFunction)){
dev.print(png, file = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG)
}else{
Try( #if it is linux like
if(exists("X11", envir=.GlobalEnv) && Sys.info()["sysname"] != "Windows" && Sys.info()["sysname"] != "Darwin"){
Try(bitmap(file = AbsGraphFileName,bg=BG,res=res))
}else{ #it is MS Windows or Mac
Try(png(filename = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG))
}
)
plotFunction()
dev.off()
}
}else if (GraphSaveAs=="jpg"){
if (is.null(plotFunction)){
dev.print(jpeg, file = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG)
}else{
Try( #if it is linux like
if (exists("X11", envir=.GlobalEnv) && Sys.info()["sysname"] != "Windows" && Sys.info()["sysname"] != "Darwin"){
Try(bitmap(filename = AbsGraphFileName,bg=BG,res=res,type="jpeg"))
}else{ #it is MS Windows or Mac
Try(jpeg(filename = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG))
}
)
plotFunction()
dev.off()
}
}else{
stop("GraphSaveAs must be either jpg, or png")
}
cat(
paste(
"<p align=",
Align,
"><img src='",
paste(GraphRelativeDirectory,"/",GraphFileName,sep=""),
"' border=",
GraphBorder,
">",
sep = "",
collapse = ""
),
file = File,
append = TRUE,
sep = ""
)
if (Caption != "") {
cat(paste("<br><i>", Caption, "</i>"), file = File, append = TRUE, sep = "")
}
cat("</P>", file = File, append = TRUE, sep = "\n")
if (exists("HTMLenv",where=".GlobalEnv",mode="environment")){
try(assign(".HTML.graph", TRUE, envir = get("HTMLenv", envir = .GlobalEnv)))
}
###try(assign(".HTML.graph", TRUE, envir = get("HTMLenv", envir = .GlobalEnv)))
invisible()
}
GetComponentsToExportInHTMLreport <- function(contrastParameterizationIndex=NULL)
# Get numberOfGenes, adjustMethod and sortBy from environment if they are available.
# Otherwise set them to default values.
{
Try(
if(exists("numberOfGenes",envir=affylmGUIenvironment)){
Try(numberOfGenes <- get("numberOfGenes",envir=affylmGUIenvironment))
if(numberOfGenes > 100)numberOfGenes <- 100 #dontplot more than 100 here
}else{
Try(numberOfGenes <- 50)
Try(assign("numberOfGenes",numberOfGenes,affylmGUIenvironment))
}
)
Try(
if(exists("sortBy",envir=affylmGUIenvironment)){
Try(sortBy <- get("sortBy",envir=affylmGUIenvironment))
}else{
Try(sortBy <- "B")
Try(assign("sortBy",sortBy,affylmGUIenvironment))
}
)
Try(
if(exists("adjustMethod",envir=affylmGUIenvironment)){
Try(adjustMethod <- get("adjustMethod",envir=affylmGUIenvironment))
}else{
Try(adjustMethod <- "BH")
Try(assign("adjustMethod",adjustMethod,affylmGUIenvironment))
}
)
Try(NumContrastParameterizations <- get("NumContrastParameterizations",envir=affylmGUIenvironment))
Try(ttHTMLreportDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttHTMLreportDialog))
Sys.sleep(0.1)
Try(tkgrab.set(ttHTMLreportDialog))
Try(tkfocus(ttHTMLreportDialog))
Try(tkwm.title(ttHTMLreportDialog,"HTML Report"))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),tklabel(ttHTMLreportDialog,text=" ")))
Try(TargetsTcl <- tclVar("1"))
Try(NormalizationMethodTcl <- tclVar("1"))
Try(RawIntensityBoxPlotTcl <- tclVar("1"))
Try(NormalizedIntensityBoxPlotTcl <- tclVar("1"))
Try(DesignMatrixTcl <- tclVar("1"))
#set ContrastMatrixTcl
Try(
if (NumContrastParameterizations>0)
Try(ContrastMatrixTcl <- tclVar("1"))
else
Try(ContrastMatrixTcl <- tclVar("0"))
)
#set MAPlotsContrastsTcl
Try(
if (NumContrastParameterizations>0)
Try(MAPlotsContrastsTcl <- tclVar("1"))
else
Try(MAPlotsContrastsTcl <- tclVar("0"))
)
#set TopNNToptablesTcl
Try(
if (NumContrastParameterizations>0)
Try(TopNNToptablesTcl <- tclVar("1"))
else
Try(TopNNToptablesTcl <- tclVar("0"))
)
#set CompleteToptablesTcl
Try(
if (NumContrastParameterizations>0)
Try(CompleteToptablesTcl <- tclVar("1"))
else
Try(CompleteToptablesTcl <- tclVar("0"))
)
#set TopNNToptablesTcl
Try(
if (NumContrastParameterizations>0)
Try(TopNNToptablesTcl <- tclVar("1"))
else
Try(TopNNToptablesTcl <- tclVar("0"))
)
#set CompleteToptablesTcl
Try(CompleteToptablesTcl <- tclVar("0"))
Try(TargetsCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=TargetsTcl))
Try(NormalizationMethodCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=NormalizationMethodTcl))
Try(RawIntensityBoxPlotCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=RawIntensityBoxPlotTcl))
Try(NormalizedIntensityBoxPlotCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=NormalizedIntensityBoxPlotTcl))
Try(DesignMatrixCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=DesignMatrixTcl))
Try(ContrastMatrixCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=ContrastMatrixTcl))
Try(MAPlotsContrastsCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=MAPlotsContrastsTcl))
Try(TopNNToptablesCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=TopNNToptablesTcl))
Try(CompleteToptablesCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=CompleteToptablesTcl))
Try(lbl2 <- tklabel(ttHTMLreportDialog,text="Components to be Included in the HTML Report",font=.affylmGUIglobals$affylmGUIfont2))
tkgrid(tklabel(ttHTMLreportDialog,text=" "),lbl2)
Try(tkgrid.configure(lbl2,columnspan=3,sticky="w"))
tkgrid(tklabel(ttHTMLreportDialog,text=" "))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="RNA Targets",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),TargetsCheckbox,currentLabel))
Try(tkgrid.configure(TargetsCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Normalization Method",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),NormalizationMethodCheckbox,currentLabel))
Try(tkgrid.configure(NormalizationMethodCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Raw Intensity Box Plot",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),RawIntensityBoxPlotCheckbox,currentLabel))
Try(tkgrid.configure(RawIntensityBoxPlotCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Normalized Intensity Box Plot",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),NormalizedIntensityBoxPlotCheckbox,currentLabel))
Try(tkgrid.configure(NormalizedIntensityBoxPlotCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Design Matrix (Parameterization)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),DesignMatrixCheckbox,currentLabel))
Try(tkgrid.configure(DesignMatrixCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Contrasts Matrix (Parameterization)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),ContrastMatrixCheckbox,currentLabel))
Try(tkgrid.configure(ContrastMatrixCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="M A Plots for Contrasts",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),MAPlotsContrastsCheckbox,currentLabel))
Try(tkgrid.configure(MAPlotsContrastsCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text=paste("Top ",numberOfGenes," DE Genes. TopTable sets Adjust Method = ",adjustMethod," sort by = ",sortBy,".",sep=""),font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),TopNNToptablesCheckbox,currentLabel))
Try(tkgrid.configure(TopNNToptablesCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Complete Lists of DE-Ranked Genes",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),CompleteToptablesCheckbox,currentLabel))
Try(tkgrid.configure(CompleteToptablesCheckbox,sticky="e"));
Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
if (NumContrastParameterizations==0){
Try(tkconfigure(ContrastMatrixCheckbox, state="disabled"))
Try(tkconfigure(MAPlotsContrastsCheckbox, state="disabled"))
Try(tkconfigure(TopNNToptablesCheckbox, state="disabled"))
Try(tkconfigure(CompleteToptablesCheckbox,state="disabled"))
}
tkgrid(tklabel(ttHTMLreportDialog,text=" "))
tkgrid(tklabel(ttHTMLreportDialog,text=" "))
ReturnVal <- list()
onOK <- function(){
if (tclvalue(TargetsTcl) =="1") ReturnVal[["Targets"]] <- TRUE else ReturnVal[["Targets"]] <- FALSE
if (tclvalue(NormalizationMethodTcl) =="1") ReturnVal[["NormalizationMethod"]] <- TRUE else ReturnVal[["NormalizationMethod"]] <- FALSE
if (tclvalue(RawIntensityBoxPlotTcl) =="1") ReturnVal[["RawIntensityBoxPlot"]] <- TRUE else ReturnVal[["RawIntensityBoxPlot"]] <- FALSE
if (tclvalue(NormalizedIntensityBoxPlotTcl)=="1") ReturnVal[["NormalizedIntensityBoxPlot"]] <- TRUE else ReturnVal[["NormalizedIntensityBoxPlot"]] <- FALSE
if (tclvalue(DesignMatrixTcl) =="1") ReturnVal[["DesignMatrix"]] <- TRUE else ReturnVal[["DesignMatrix"]] <- FALSE
if (tclvalue(ContrastMatrixTcl) =="1") ReturnVal[["ContrastsMatrix"]] <- TRUE else ReturnVal[["ContrastsMatrix"]] <- FALSE
if (tclvalue(MAPlotsContrastsTcl) =="1") ReturnVal[["MAPlotsContrasts"]] <- TRUE else ReturnVal[["MAPlotsContrasts"]] <- FALSE
if (tclvalue(TopNNToptablesTcl) =="1") ReturnVal[["TopNNToptablesTcl"]] <- TRUE else ReturnVal[["TopNNToptables"]] <- FALSE
if (tclvalue(CompleteToptablesTcl) =="1") ReturnVal[["CompleteToptablesTcl"]] <- TRUE else ReturnVal[["CompleteToptablesTcl"]] <- FALSE
Try(tkgrab.release(ttHTMLreportDialog));
Try(tkdestroy(ttHTMLreportDialog));
Try(tkfocus(.affylmGUIglobals$ttMain))
ReturnVal <<- ReturnVal
}
onCancel <- function(){
Try(tkgrab.release (ttHTMLreportDialog));
Try(tkdestroy (ttHTMLreportDialog));
Try(tkfocus (.affylmGUIglobals$ttMain));
ReturnVal <<- list()
}
OK.but <-tkbutton(ttHTMLreportDialog,text=" OK ",command=onOK, font=.affylmGUIglobals$affylmGUIfont2)
Cancel.but <-tkbutton(ttHTMLreportDialog,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2)
tkgrid(tklabel(ttHTMLreportDialog,text=" "),tklabel(ttHTMLreportDialog,text=" "),OK.but,Cancel.but,tklabel(ttHTMLreportDialog,text=" "),tklabel(ttHTMLreportDialog,text=" "))
tkgrid.configure(OK.but, sticky="e")
tkgrid.configure(Cancel.but,sticky="w")
tkgrid(
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" ")
)
Try(tkfocus(ttHTMLreportDialog))
Try(tkbind(ttHTMLreportDialog, "<Destroy>", function() {Try(tkgrab.release(ttHTMLreportDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttHTMLreportDialog))
return (ReturnVal)
}
ExportHTMLreport <- function(){
# We will use the R2HTML package, but with my own HTMLplot function.
# Will we need xtable or does R2HTML have its own HTMLtable function?
#get numberOfGenes,adjustMethod and sortBy from environment if they are available, if not, set them to default values
Try(
if(exists("numberOfGenes",envir=affylmGUIenvironment)){
Try(numberOfGenes <- get("numberOfGenes",envir=affylmGUIenvironment))
if(numberOfGenes > 100)numberOfGenes <- 100 #dontplot more than 100 here
}else{
Try(numberOfGenes <- 50)
Try(assign("numberOfGenes",numberOfGenes,affylmGUIenvironment))
}
)
Try(
if(exists("sortBy",envir=affylmGUIenvironment)){
Try(sortBy <- get("sortBy",envir=affylmGUIenvironment))
}else{
Try(sortBy <- "B")
Try(assign("sortBy",sortBy,affylmGUIenvironment))
}
)
Try(
if(exists("adjustMethod",envir=affylmGUIenvironment)){
Try(adjustMethod <- get("adjustMethod",envir=affylmGUIenvironment))
}else{
Try(adjustMethod <- "BH")
Try(assign("adjustMethod",adjustMethod,affylmGUIenvironment))
}
)
Try(limmaDataSetNameText <- get("limmaDataSetNameText" ,envir=affylmGUIenvironment)) #for eg: [1] "alg_Est_gcrma_3C"
Try(ArraysLoaded <- get("ArraysLoaded" , envir=affylmGUIenvironment))
Try(NumContrastParameterizations <- get("NumContrastParameterizations" ,envir=affylmGUIenvironment)) #for eg: [1] 1
Try(ContrastParameterizationList <- get("ContrastParameterizationList" ,envir=affylmGUIenvironment))
# for eg:
#> summary(ContrastParameterizationList)
# Length Class Mode
#ContrastParameterizationName.1 5 -none- list
#ContrastParameterizationList is a list with entrys for each gene(?) for:
#some values for each gene off the top of the screen, followed by all of this data:
#$ContrastParameterizationName.1$eb$rank
#[1] 4
#$ContrastParameterizationName.1$eb$assign
#NULL
#$ContrastParameterizationName.1$eb$qr
#$qr
# EstAbsent10 EstAbsent48 EstPresent10 EstPresent48
#low10-1.cel -1.4142136 0.0000000 0.0000000 0.0000000
#low10-2.cel 0.7071068 -1.4142136 0.0000000 0.0000000
#high10-1.cel 0.0000000 0.0000000 -1.4142136 0.0000000
#high10-2.cel 0.0000000 0.0000000 0.7071068 -1.4142136
#low48-1.cel 0.0000000 0.7071068 0.0000000 0.0000000
#low48-2.cel 0.0000000 0.7071068 0.0000000 0.0000000
#high48-1.cel 0.0000000 0.0000000 0.0000000 0.7071068
#high48-2.cel 0.0000000 0.0000000 0.0000000 0.7071068
#$qraux
#[1] 1.707107 1.000000 1.707107 1.000000
#$pivot
#[1] 1 2 3 4
#$tol
#[1] 1e-07
#$rank
#[1] 4
#attr(,"class")
#[1] "qr"
#$ContrastParameterizationName.1$eb$df.residual
# [1] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
# [85] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
# ... ...................................
#[12601] 4 4 4 ...
#$ContrastParameterizationName.1$eb$sigma
# 100_g_at 1000_at 1001_at 1002_f_at 1003_s_at 1004_at
# 0.210371658 0.229581752 0.056224969 0.079154826 0.035168585 0.062620730
# 1005_at 1006_at 1007_s_at 1008_f_at 1009_at 101_at
# ... ... ... ... ... ...
#$ContrastParameterizationName.1$eb$cov.coefficients
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#(EstAbsent10)-(EstAbsent48) 1.0 0.0 0.5
#(EstPresent10)-(EstPresent48) 0.0 1.0 0.5
#(EstAbsent10)-(EstPresent48) 0.5 0.5 1.0
#$ContrastParameterizationName.1$eb$stdev.unscaled
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#100_g_at 1 1 1
#1000_at 1 1 1
# ... ... ... ...
#$ContrastParameterizationName.1$eb$contrasts
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#EstAbsent10 1 0 1
#EstAbsent48 -1 0 0
#EstPresent10 0 1 0
#EstPresent48 0 -1 -1
#$ContrastParameterizationName.1$eb$df.prior
#[1] 1.916164
#$ContrastParameterizationName.1$eb$s2.prior
#[1] 0.01619520
#$ContrastParameterizationName.1$eb$var.prior
#[1] 156.9730 123.4235 256.8846
#$ContrastParameterizationName.1$eb$proportion
#[1] 0.01
#$ContrastParameterizationName.1$eb$s2.post
# 100_g_at 1000_at 1001_at 1002_f_at 1003_s_at 1004_at
# 0.035167654 0.040881861 0.007382765 0.009481584 0.006081640 0.007896685
# 1005_at 1006_at 1007_s_at 1008_f_at 1009_at 101_at
# 0.031434553 0.009843242 0.042246541 0.501898805 0.061243025 0.008799333
# ... ... ... ... ... ...
#AND
#$ContrastParameterizationName.1$eb$t
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#100_g_at 1.030421e+00 -8.576221e-01 1.325653e+00
#1000_at -7.997174e-01 -2.053407e+00 6.645345e-02
# ... ... ...
# AND
#$ContrastParameterizationName.1$eb$p.value
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#100_g_at 3.430840e-01 4.244753e-01 2.338416e-01
#1000_at 4.547765e-01 8.650180e-02 9.492055e-01
# ... ... ...
#AND
#$ContrastParameterizationName.1$eb$lods
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
# ... ... ...
#AND
#$ContrastParameterizationName.1$contrastsMatrixInList
#$ContrastParameterizationName.1$contrastsMatrixInList$contrasts
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#EstAbsent10 1 0 1
#EstAbsent48 -1 0 0
#EstPresent10 0 1 0
#EstPresent48 0 -1 -1
#$ContrastParameterizationName.1$contrastsMatrixInList$contrastsCreatedFromDropDowns
#[1] TRUE
#$ContrastParameterizationName.1$contrastsMatrixInList$Param1
#[1] 1 3 1
#$ContrastParameterizationName.1$contrastsMatrixInList$Param2
#[1] 2 4 4
#$ContrastParameterizationName.1$ContrastParameterizationNameText
#[1] "ContSet1"
Try(ContrastParameterizationTREEIndexVec <- get("ContrastParameterizationTREEIndexVec",envir=affylmGUIenvironment)) #for eg: [1] 1
if(ArraysLoaded==FALSE){
Try(tkmessageBox(title="Export HTML Report",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
if(NumContrastParameterizations>0){
#Select which parameterization
Try(contrastParameterizationIndex <- ChooseContrastParameterization()) #for eg: [1] 1
#If click cancel button, then exit this routine
Try(if (contrastParameterizationIndex==0) return()) # Cancel
Try(ContrastParameterizationNamesVec <- get("ContrastParameterizationNamesVec",envir=affylmGUIenvironment)) #for eg: [1] "ContSet1"
#store locally TREEindex for chosen parameterization
Try(.affylmGUIglobals$ContrastParameterizationTREEIndex <- ContrastParameterizationTREEIndexVec[contrastParameterizationIndex]) #for eg: [1] 1
#setup contrast matrix
Try(contrastsMatrix <- as.matrix(ContrastParameterizationList[[contrastParameterizationIndex]]$contrastsMatrixInList$contrasts))
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#EstAbsent10 1 0 1
#EstAbsent48 -1 0 0
#EstPresent10 0 1 0
#EstPresent48 0 -1 -1
#>
#get vector of names for contrasts
Try(ContrastNamesVec <- colnames(contrastsMatrix))
#for eg: [1] "(EstAbsent10)-(EstAbsent48)" "(EstPresent10)-(EstPresent48)" "(EstAbsent10)-(EstPresent48)"
Try(NumContrasts <- length(ContrastNamesVec)) #for eg: 3
Try(ContrastParameterizationNameNode <- paste("ContrastParameterizationName.",.affylmGUIglobals$ContrastParameterizationTREEIndex,sep=""))
#for eg: "ContrastParameterizationName.1"
Try(fit <- (ContrastParameterizationList[[ContrastParameterizationNameNode]])$fit)
#> summary(fit)
# Length Class Mode
#coefficients 37875 -none- numeric
#rank 1 -none- numeric
#assign 0 -none- NULL
#qr 5 qr list
#df.residual 12625 -none- numeric
#sigma 12625 -none- numeric
#cov.coefficients 9 -none- numeric
#stdev.unscaled 37875 -none- numeric
#contrasts 12 -none- numeric
#Amean 12625 -none- numeric
Try(fit <- eBayes(fit))
#> summary(fit)
# Length Class Mode
#coefficients 37875 -none- numeric
#rank 1 -none- numeric
#assign 0 -none- NULL
#qr 5 qr list
#df.residual 12625 -none- numeric
#sigma 12625 -none- numeric
#cov.coefficients 9 -none- numeric
#stdev.unscaled 37875 -none- numeric
#contrasts 12 -none- numeric
#Amean 12625 -none- numeric
#df.prior 1 -none- numeric
#s2.prior 1 -none- numeric
#var.prior 3 -none- numeric
#proportion 1 -none- numeric
#s2.post 12625 -none- numeric
#t 37875 -none- numeric
#p.value 37875 -none- numeric
#lods 37875 -none- numeric
Try(ComponentsToExport <- GetComponentsToExportInHTMLreport(contrastParameterizationIndex))
}else{
Try(ComponentsToExport <- GetComponentsToExportInHTMLreport())
}
#if nothing selected, exit this routine
Try(if (length(ComponentsToExport)==0) return())
#Setup files to use for HTML report
Try(fileNameWithPath<- tkgetSaveFile(initialfile=limmaDataSetNameText,filetypes="{{HTML Files} {.html .htm}} {{All files} *}"))
#for eg: W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C
#Try(tkmessageBox(title="229:affylmGUI-htmlreport",message=paste("fileNameWithPath =",fileNameWithPath),icon="info",default="ok"))
#if null filename selected, exit this routine
Try(if (nchar(tclvalue(fileNameWithPath))==0)return())
Try(path <- tclvalue(tclfile.dir (tclvalue(fileNameWithPath)))) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files"
#Try(tkmessageBox(title="235:affylmGUI-htmlreport",message=paste("path =",path),icon="info",default="ok"))
Try(fileName <- tclvalue(tclfile.tail(tclvalue(fileNameWithPath)))) #for eg: "alg_Est_gcrma_3C"
#Try(tkmessageBox(title="242:affylmGUI-htmlreport",message=paste("fileName =",fileName),icon="info",default="ok"))
Try(len <- nchar(fileName))
if (len<4){
Try(fileName <- paste(fileName,".html",sep=""))
}else if((tolower(substring(fileName,len-4,len))!=".html") &&(len<5 || (tolower(substring(fileName,len-4,len))!=".html"))){
Try(fileName <- paste(fileName,".html",sep="")) #for eg: "alg_Est_gcrma_3C.html"
}
Try(fileNameWithoutExtension <- substring(fileName,1,nchar(fileName)-5)) #for eg: "alg_Est_gcrma_3C"
Try(HTMLfilePath <- paste(path,.Platform$file.sep,fileNameWithoutExtension,"_files",sep="")) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C_files"
Try(HTMLfileRelativePath <- paste(fileNameWithoutExtension,"_files",sep="")) #for eg: "alg_Est_gcrma_3C_files"
Try(dir.create(HTMLfilePath))
Try(fileNameWithPath <- paste(path,"/",fileName,sep="")) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C.html"
Try(R2HTMLpath <- system.file(package="R2HTML","output")) #for eg: [1] "C:/R/R-2.6.0alpha/library/R2HTML/output"
Try(cssFileSource <- paste(R2HTMLpath,"/","R2HTML.css",sep="")) #for eg: [1] "C:/R/R-2.6.0alpha/library/R2HTML/output/R2HTML.css"
Try(cssFileDestination <- paste(path,"/","R2HTML.css",sep="")) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/R2HTML.css"
Try(R2HTMLlogoSource <- paste(R2HTMLpath,"/","R2HTMLlogo.png",sep="")) #for eg: [1] "C:/R/R-2.6.0alpha/library/R2HTML/output/R2HTMLlogo.png"
Try(R2HTMLlogoDestination <- paste(path,"/","R2HTMLlogo.png",sep="")) #for eg: [1] "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/R2HTMLlogo.png"
Try(file.copy(cssFileSource,cssFileDestination,overwrite=TRUE)) #for eg: TRUE
Try(file.copy(R2HTMLlogoSource,R2HTMLlogoDestination,overwrite=TRUE)) #for eg: TRUE
Try(HTMLtarget <- HTMLInitFile(path,filename=fileNameWithoutExtension,Title=paste(limmaDataSetNameText,"- Statistical Microarray Analysis using affylmGUI"), HTMLframe=FALSE,BackGroundColor="#FFFFFF"))
# for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C.html"
# The following is written to this file:
# <html xmlns:mml="http://www.w3.org/1998/Math/MathML">
# <head>
# <title> alg_Est_gcrma_3C - Statistical Microarray Analysis using affylmGUI </title>
# <link rel=stylesheet href="R2HTML.css" type=text/css>
# <object id="mathplayer" classid="clsid:32F66A20-7614-11D4-BD11-00104BD3F987"></object>
# <?import namespace="mml" implementation="#mathplayer"?>
# <script type="text/javascript" src="ASCIIMathML.js"></script>
# <link href="./runtime/styles/xp/grid.css" rel="stylesheet" type="text/css" ></link>
# <link href="gridR2HTML.css" rel="stylesheet" type="text/css" ></link>
# <script src="./runtime/lib/grid.js"></script>
# <script src="./gridR2HTML.js"></script>
# <script>
# nequations=0;
# </script>
# </head>
# <body onload="translate()" bgcolor= #FFFFFF background="" >
Try(HTML.title(paste(limmaDataSetNameText,"- Statistical Microarray Analysis using affylmGUI"),HR=1)) #for eg: NULL
# for eg: written to html file is:
# <h1 > alg_Est_gcrma_3C - Statistical Microarray Analysis using affylmGUI</h1>
Try(ExportTargets <- ComponentsToExport$Targets)
Try(ExportNormalizationMethod <- ComponentsToExport$NormalizationMethod)
Try(ExportRawIntensityBoxPlot <- ComponentsToExport$RawIntensityBoxPlot)
Try(ExportNormalizedIntensityBoxPlot <- ComponentsToExport$NormalizedIntensityBoxPlot)
Try(ExportDesignMatrix <- ComponentsToExport$DesignMatrix)
Try(ExportContrastsMatrix <- ComponentsToExport$ContrastsMatrix)
Try(ExportMAPlotsContrasts <- ComponentsToExport$MAPlotsContrasts)
Try(ExportTopNNToptables <- ComponentsToExport$TopNNToptables)
Try(ExportCompleteToptables <- ComponentsToExport$CompleteToptables)
#All the above are set to TRUE or FALSE, depending on what was chosen in the dialogue box
#This sets up parameters for the plots
if(ExportRawIntensityBoxPlot || ExportNormalizedIntensityBoxPlot || ExportMAPlotsContrasts){
Try(
#if linux like
if (exists("X11", envir=.GlobalEnv) && Sys.info()["sysname"] != "Windows" && Sys.info()["sysname"] != "Darwin"){
Try(pngParams <- GetJpegOrPngX11Params(graphFileType="PNG")) #sets background colour(bg) and resolution(res)
Try(if (length(pngParams)==0) return())
Try(plotBG <- pngParams$bg)
Try(plotRes <- pngParams$res)
}else{
#if Windows or Mac
Try(pngParams <- GetJpegOrPngParams(graphFileType="PNG")) #sets width, height, background colour(bg) and Font Size(pointsize)
Try(if (length(pngParams)==0) return())
Try(plotWidth <- pngParams$width)
Try(plotHeight <- pngParams$height)
Try(plotPointSize <- pngParams$pointsize)
Try(plotBG <- pngParams$bg)
}
)
}
Try(HTML.title("Contents",HR=2)) # this writes " <h2 > Contents</h2>" to html file
#This writes links to html file for each feature selected
Try(if (ExportTargets) Try(HTMLli(txt="<a href=\"#Targets\"><b>Targets</b></a>")))
Try(if (ExportNormalizationMethod) Try(HTMLli(txt="<a href=\"#NormalizationMethod\"><b>Normalization Method</b></a>")))
Try(if (ExportRawIntensityBoxPlot) Try(HTMLli(txt="<a href=\"#RawIntensityBoxPlot\"><b>Raw Intensity Box Plot</b></a>")))
Try(if (ExportNormalizedIntensityBoxPlot) Try(HTMLli(txt="<a href=\"#NormalizedIntensityBoxPlot\"><b>Normalized Intensity Box Plot</b></a>")))
Try(if (ExportDesignMatrix) Try(HTMLli(txt="<a href=\"#DesignMatrix\"><b>Design Matrix</b></a>")))
Try(if (ExportContrastsMatrix) Try(HTMLli(txt="<a href=\"#ContrastsMatrix\"><b>Contrasts Matrix</b></a>")))
Try(if (ExportMAPlotsContrasts) Try(HTMLli(txt="<a href=\"#MAPlotsContrasts\"><b>M A Plots for Contrasts</b></a>")))
Try(if (ExportTopNNToptables) Try(HTMLli(txt=paste("<a href=\"#TopNNToptables\"><b>Tables of Top ",numberOfGenes," Differentially Expressed Genes</b></a>",sep=""))))
Try(if (ExportCompleteToptables) Try(HTMLli(txt="<a href=\"#CompleteToptables\"><b>Complete Tables of Genes Ranked in order of Evidence for Differential Expression</b></a>")))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkfocus(.affylmGUIglobals$ttMain))
if (ExportTargets){
Try(Targets <- get("Targets",envir=affylmGUIenvironment))
#for eg: Targets is:
# Name FileName Target
#1 Abs10.1 low10-1.cel EstAbsent10
#2 Abs10.2 low10-2.cel EstAbsent10
#3 Pres10.1 high10-1.cel EstPresent10
#4 Pres10.2 high10-2.cel EstPresent10
#5 Abs48.1 low48-1.cel EstAbsent48
#6 Abs48.2 low48-2.cel EstAbsent48
#7 Pres48.1 high48-1.cel EstPresent48
#8 Pres48.2 high48-2.cel EstPresent48
Try(displayVector <- rep("s",ncol(Targets)+1)) #for eg: [1] "s" "s" "s" "s"
Try(
for (i in (0:ncol(Targets))){
if (i==0 || colnames(Targets)[i]=="SlideNumber"){
displayVector[i] <- "d"
}
}
)
#for eg: This has set the displayVector to [1] "s" "s" "s" "s"
Try(TargetsXtable <- xtable(Targets,display=displayVector))
# for eg: This outputs:
# % latex table generated in R 2.6.0 by xtable 1.5-1 package
# % Thu Sep 20 16:44:04 2007
# \begin{table}[ht]
# \begin{center}
# \begin{tabular}{rlll}
# \hline
# & Name & FileName & Target \\
# \hline
# 1 & Abs10.1 & low10-1.cel & EstAbsent10 \\
# 2 & Abs10.2 & low10-2.cel & EstAbsent10 \\
# 3 & Pres10.1 & high10-1.cel & EstPresent10 \\
# 4 & Pres10.2 & high10-2.cel & EstPresent10 \\
# 5 & Abs48.1 & low48-1.cel & EstAbsent48 \\
# 6 & Abs48.2 & low48-2.cel & EstAbsent48 \\
# 7 & Pres48.1 & high48-1.cel & EstPresent48 \\
# 8 & Pres48.2 & high48-2.cel & EstPresent48 \\
# \hline
# \end{tabular}
# \end{center}
# \end{table}
Try(HTML.title("<a name=\"Targets\">RNA Targets</a>",HR=2)) #for eg: this writes " <h2 > <a name="Targets">RNA Targets</a></h2>" to html file
Try(print(TargetsXtable,type="html",file=fileNameWithPath,append=TRUE))
#For eg: This prints the following to the html file:
# <!-- Thu Sep 20 16:46:24 2007 -->
# <TABLE border=1>
# <TR> <TH> </TH> <TH> Name </TH> <TH> FileName </TH> <TH> Target </TH> </TR>
# <TR> <TD align="right"> 1 </TD> <TD> Abs10.1 </TD> <TD> low10-1.cel </TD> <TD> EstAbsent10 </TD> </TR>
# <TR> <TD align="right"> 2 </TD> <TD> Abs10.2 </TD> <TD> low10-2.cel </TD> <TD> EstAbsent10 </TD> </TR>
# <TR> <TD align="right"> 3 </TD> <TD> Pres10.1 </TD> <TD> high10-1.cel </TD> <TD> EstPresent10 </TD> </TR>
# <TR> <TD align="right"> 4 </TD> <TD> Pres10.2 </TD> <TD> high10-2.cel </TD> <TD> EstPresent10 </TD> </TR>
# <TR> <TD align="right"> 5 </TD> <TD> Abs48.1 </TD> <TD> low48-1.cel </TD> <TD> EstAbsent48 </TD> </TR>
# <TR> <TD align="right"> 6 </TD> <TD> Abs48.2 </TD> <TD> low48-2.cel </TD> <TD> EstAbsent48 </TD> </TR>
# <TR> <TD align="right"> 7 </TD> <TD> Pres48.1 </TD> <TD> high48-1.cel </TD> <TD> EstPresent48 </TD> </TR>
# <TR> <TD align="right"> 8 </TD> <TD> Pres48.2 </TD> <TD> high48-2.cel </TD> <TD> EstPresent48 </TD> </TR>
# </TABLE>
# <!-- html table generated in R 2.6.0 by xtable 1.5-1 package -->
}
if (ExportNormalizationMethod){
Try(NormMethod <- get("NormMethod", envir=affylmGUIenvironment)) #for eg: GCRMA
Try(HTML.title("<a name=\"NormalizationMethod\">Normalization method</a>",HR=2)) #writes to html: " <h2 > <a name="NormalizationMethod">Normalization method</a></h2>"
Try(
if(NormMethod=="RMA"){
Try(HTMLli(txt="<b>RMA (Robust Multiarray Averaging)</b>"))
}else if(NormMethod=="PLM"){
Try(HTMLli(txt="<b>PLM (Robust Probe-level Linear Model)</b>"))
}else if(NormMethod=="GCRMA"){
Try(HTMLli(txt="<b>GCRMA (GC Robust Multiarray Averaging)</b>"))
}else{
Try(HTMLli(txt="<b>UnKnown (Unrecognised method - check with package maintainer)</b>"))
}
) #which writes to the html file for eg: "<br><li><b>GCRMA (GC Robust Multiarray Averaging)</b>"
}
if(ExportRawIntensityBoxPlot){
Try(HTML.title("<a name=\"RawIntensityBoxPlot\">Raw (Unnormalized) Intensity Box Plot</a>",HR=2))
#which writes for eg: <h2 > <a name="RawIntensityBoxPlot">Raw (Unnormalized) Intensity Box Plot</a></h2>
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
#for eg: this is:
#AffyBatch object
#size of arrays=640x640 features (8 kb)
#cdf=HG_U95Av2 (12625 affyids)
#number of samples=8
#number of genes=12625
#annotation=hgu95av2
#notes=
Try(SlideNamesVec <- get("SlideNamesVec",envir=affylmGUIenvironment)) #for eg: [1] "Abs10.1" "Abs10.2" "Pres10.1" "Pres10.2" "Abs48.1" "Abs48.2" "Pres48.1" "Pres48.2"
#This plotFunction creates a boxplot from the raw data
Try(
plotFunction <- function(){
Try(opar<-par(bg="white",cex=0.7))
Try(boxplot(RawAffyData,col="red",las=2,names=SlideNamesVec))
Try(title(plotTitle))
Try(tmp<-par(opar))
}
)
Try(plotTitle <- "Raw intensity distribution for each slide")
Try(
HTMLplotUsingFunction(
Caption = plotTitle,
File = fileNameWithPath,
GraphRelativeDirectory = HTMLfileRelativePath ,
GraphAbsoluteDirectory = HTMLfilePath,
GraphFileName = "RawIntensityBoxPlot",
GraphSaveAs = "png",
GraphBorder = 1,
Align = "left",
plotFunction = plotFunction,
Width = plotWidth,
Height = plotHeight,
PointSize = plotPointSize,
BG = plotBG,
res = plotRes
)
)
#For eg: This writes to the html file:
# <p align=left><img src='alg_Est_gcrma_3C_files/RawIntensityBoxPlot.png' border=1><br><i> Raw intensity distribution for each slide </i></P>
#and creates a file "RawIntensityBoxPlot.png" in the "alg_Est_gcrma_3C_files" subdirectory.
}
if(ExportNormalizedIntensityBoxPlot){
Try(HTML.title("<a name=\"NormalizedIntensityBoxPlot\">Normalized Intensity Box Plot</a>",HR=2))
# for eg: this writes to the HTML file:
# <h2 > <a name="NormalizedIntensityBoxPlot">Normalized Intensity Box Plot</a></h2>
Try(NormalizedAffyData.exprs <- get("NormalizedAffyData.exprs",envir=affylmGUIenvironment))
#For eg: this is the normalized data:
#> summary(NormalizedAffyData.exprs)
# low10-1.cel low10-2.cel high10-1.cel high10-2.cel low48-1.cel low48-2.cel high48-1.cel high48-2.cel
# Min. :-0.3586 Min. :-0.3778 Min. :-0.2799 Min. :-0.2883 Min. :-0.3431 Min. :-0.3487 Min. :-0.3648 Min. :-0.3192
# 1st Qu.: 2.8701 1st Qu.: 2.8529 1st Qu.: 3.0408 1st Qu.: 3.1354 1st Qu.: 2.8521 1st Qu.: 2.9442 1st Qu.: 2.8054 1st Qu.: 2.9633
# Median : 4.0612 Median : 4.0319 Median : 4.1881 Median : 4.2567 Median : 3.9914 Median : 4.0573 Median : 3.9331 Median : 4.0457
# Mean : 5.1289 Mean : 5.0827 Mean : 5.2261 Mean : 5.2530 Mean : 5.0292 Mean : 4.9990 Mean : 5.0386 Mean : 5.0201
# 3rd Qu.: 7.2458 3rd Qu.: 7.1482 3rd Qu.: 7.2749 3rd Qu.: 7.2045 3rd Qu.: 7.0249 3rd Qu.: 6.8045 3rd Qu.: 7.1026 3rd Qu.: 6.8093
# Max. :16.0300 Max. :16.0264 Max. :15.8995 Max. :15.9624 Max. :15.9858 Max. :15.9348 Max. :15.6545 Max. :15.7622
Try(SlideNamesVec <- get("SlideNamesVec",envir=affylmGUIenvironment))
#for eg: SlideNamesVec is:
#[1] "Abs10.1" "Abs10.2" "Pres10.1" "Pres10.2" "Abs48.1" "Abs48.2" "Pres48.1" "Pres48.2"
#This plotFunction will create a boxplot of Normalized data
Try(
plotFunction <- function(){
Try(opar<-par(bg="white",cex=0.7))
Try(boxplot(data.frame(NormalizedAffyData.exprs),col="blue",las=2,names=SlideNamesVec))
Try(title(plotTitle))
Try(tmp<-par(opar))
}
)
Try(plotTitle<-"Normalized intensity distribution for each slide")
Try(
HTMLplotUsingFunction(
Caption = plotTitle,
File = fileNameWithPath,
GraphRelativeDirectory = HTMLfileRelativePath,
GraphAbsoluteDirectory = HTMLfilePath,
GraphFileName = "NormalizedIntensityBoxPlot",
GraphSaveAs = "png",
GraphBorder = 1,
Align = "left",
plotFunction=plotFunction,
Width=plotWidth,
Height=plotHeight,
PointSize=plotPointSize,
BG=plotBG,
res=plotRes
)
)
#For eg: This writes to HTML file:
# <p align=left><img src='alg_Est_gcrma_3C_files/NormalizedIntensityBoxPlot.png' border=1><br><i> Normalized intensity distribution for each slide </i></P>
#It also creates the file "NormalizedIntensityBoxPlot.png" in the "alg_Est_gcrma_3C_files" subdirectory.
}
if(ExportDesignMatrix){
Try(design <- get("design",envir=affylmGUIenvironment))
#For eg: This gets the design matrix:
# EstAbsent10 EstAbsent48 EstPresent10 EstPresent48
#low10-1.cel 1 0 0 0
#low10-2.cel 1 0 0 0
#high10-1.cel 0 0 1 0
#high10-2.cel 0 0 1 0
#low48-1.cel 0 1 0 0
#low48-2.cel 0 1 0 0
#high48-1.cel 0 0 0 1
#high48-2.cel 0 0 0 1
Try(displayVector <- rep("g",ncol(design)+1)) #This creates: [1] "g" "g" "g" "g" "g"
Try(displayVector[0] <- "s")
Try(DesignXtable <- xtable(design,display=displayVector))
#For eg. This creates:
#% latex table generated in R 2.6.0 by xtable 1.5-1 package
#% Thu Sep 20 22:42:27 2007
#\begin{table}[ht]
#\begin{center}
#\begin{tabular}{rrrrr}
# \hline
# & EstAbsent10 & EstAbsent48 & EstPresent10 & EstPresent48 \\
# \hline
#low10-1.cel & 1 & 0 & 0 & 0 \\
# low10-2.cel & 1 & 0 & 0 & 0 \\
# high10-1.cel & 0 & 0 & 1 & 0 \\
# high10-2.cel & 0 & 0 & 1 & 0 \\
# low48-1.cel & 0 & 1 & 0 & 0 \\
# low48-2.cel & 0 & 1 & 0 & 0 \\
# high48-1.cel & 0 & 0 & 0 & 1 \\
# high48-2.cel & 0 & 0 & 0 & 1 \\
# \hline
#\end{tabular}
#\end{center}
#\end{table}
Try(HTML.title("<a name=\"DesignMatrix\">Design Matrix</a>",HR=2))
# For eg. this writes to HTML file:
# <h2 > <a name="DesignMatrix">Design Matrix</a></h2>
Try(print(DesignXtable,type="html",file=fileNameWithPath,append=TRUE))
#For eg. This writes to HTML file:
#<!-- html table generated in R 2.6.0 by xtable 1.5-1 package -->
#<!-- Thu Sep 20 22:44:52 2007 -->
#<TABLE border=1>
#<TR> <TH> </TH> <TH> EstAbsent10 </TH> <TH> EstAbsent48 </TH> <TH> EstPresent10 </TH> <TH> EstPresent48 </TH> </TR>
# <TR> <TD align="right"> low10-1.cel </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> low10-2.cel </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> high10-1.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> high10-2.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> low48-1.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> low48-2.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> high48-1.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> </TR>
# <TR> <TD align="right"> high48-2.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> </TR>
# </TABLE>
}
if(ExportContrastsMatrix){
Try(displayVector <- rep("g",ncol(contrastsMatrix)+1))
Try(displayVector[0] <- "s")
Try(ContrastsXtable <- xtable(contrastsMatrix,display=displayVector))
Try(HTML.title("<a name=\"ContrastsMatrix\">Contrasts Matrix</a>",HR=2))
Try(print(ContrastsXtable,type="html",file=fileNameWithPath,append=TRUE))
#For eg. In a similar wat to design table, this routine writes this to the HTML file:
# <h2 > <a name="ContrastsMatrix">Contrasts Matrix</a></h2><!-- html table generated in R 2.6.0 by xtable 1.5-1 package -->
#<!-- Thu Sep 20 22:46:48 2007 -->
#<TABLE border=1>
#<TR> <TH> </TH> <TH> (EstAbsent10)-(EstAbsent48) </TH> <TH> (EstPresent10)-(EstPresent48) </TH> <TH> (EstAbsent10)-(EstPresent48) </TH> </TR>
# <TR> <TD align="right"> EstAbsent10 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> </TR>
# <TR> <TD align="right"> EstAbsent48 </TD> <TD align="right"> -1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> EstPresent10 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> EstPresent48 </TD> <TD align="right"> 0 </TD> <TD align="right"> -1 </TD> <TD align="right"> -1 </TD> </TR>
# </TABLE>
}
if(ExportMAPlotsContrasts){
Try(HTML.title("<a name=\"MAPlotsContrasts\">M A Plots for Contrasts</a>",HR=2))
#For eg. This writes to HTML file:
# <h2 > <a name="MAPlotsContrasts">M A Plots for Contrasts</a></h2>
Try(A <- rowMeans(NormalizedAffyData.exprs))
#For eg. This gets rowMeans, as summarized below:
#> summary(A)
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#-0.3351 2.9500 4.1050 5.0970 7.0480 15.9100
Try(pch <- 16) #set character height plot
Try(cex <- 0.2) #set character expansion for plot
Try(
#In this example, create an MA plot for each of the three contrast
for (contrast in (1:NumContrasts)){ #For eg. NumContrasts = 3
Try(plotTitle<-paste("M A Plot (",ContrastNamesVec[contrast],")",sep="")) # ContrastNamesVec = "(EstAbsent10)-(EstAbsent48)" "(EstPresent10)-(EstPresent48)" "(EstAbsent10)-(EstPresent48)"
Try(HTML.title(plotTitle,HR=2))
#For eg. this writes to HTML:
# <h2 > M A Plot ((EstAbsent10)-(EstAbsent48))</h2><p align=left><img src='alg_Est_gcrma_3C_files/contrastMAplot.1.png' border=1><br><i> M A Plot ((EstAbsent10)-(EstAbsent48)) </i></P>
# <h2 > M A Plot ((EstPresent10)-(EstPresent48))</h2><p align=left><img src='alg_Est_gcrma_3C_files/contrastMAplot.2.png' border=1><br><i> M A Plot ((EstPresent10)-(EstPresent48)) </i></P>
# <h2 > M A Plot ((EstAbsent10)-(EstPresent48))</h2><p align=left><img src='alg_Est_gcrma_3C_files/contrastMAplot.3.png' border=1><br><i> M A Plot ((EstAbsent10)-(EstPresent48)) </i></P>
Try(M <- fit$coefficients[,contrast])
#For eg. For contrast no.1, M is:
#> summary(M)
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#-5.303e+00 -9.561e-02 7.819e-05 9.169e-02 2.857e-01 1.168e+01
#> length(M)
#[1] 12625
#Do an MA plot
Try(
plotFunction <- function(){
Try(opar<-par(bg="white"))
Try(plot(A,M,pch=pch,cex=cex,xlab="A",ylab="M",main=plotTitle))
Try(tmp<-par(opar))
}
)
Try(
HTMLplotUsingFunction(
Caption = plotTitle,
File = fileNameWithPath,
GraphRelativeDirectory = HTMLfileRelativePath,
GraphAbsoluteDirectory = HTMLfilePath,
GraphFileName = paste("contrastMAplot.",contrast,sep=""),
GraphSaveAs = "png",
GraphBorder = 1,
Align = "left",
plotFunction=plotFunction,
Width=plotWidth,
Height=plotHeight,
PointSize=plotPointSize,
BG=plotBG,
res=plotRes
)
)
}
)
}
if(ExportTopNNToptables || ExportCompleteToptables){
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
Try(cdfName <- strsplit(cleancdfname(cdfName(RawAffyData)),"cdf")[[1]])
if(!(.cdfName2AnnPkg(cdfName) %in% .packages(all.available=TRUE))){
Try(install.packages(pkgs=.cdfName2AnnPkg(cdfName), lib=.libPaths(), repos=repositories(), dependencies=c("Depends", "Imports")))
Try(assign("cdfName",cdfName,affylmGUIenvironment))
}
Try(cdfenv <- getCdfInfo(RawAffyData))
Try(genelist <- data.frame(ID=I(ls(cdfenv))))
Try(geneNames <- get("geneNames", envir=affylmGUIenvironment))
Try(geneSymbols <- get("geneSymbols",envir=affylmGUIenvironment))
Try(
if(!length(geneNames) || !length(geneSymbols)){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
Try(cdfName <- strsplit(cleancdfname(cdfName(RawAffyData)),"cdf")[[1]])
if(!(cdfName %in% .packages(all.available=TRUE))){
Try(install.packages(pkgs=.cdfName2AnnPkg(cdfName), lib=.libPaths(), repos=repositories(), dependencies=c("Depends", "Imports")))###inserted by keith
}
Try(
if( (.cdfName2AnnPkg(cdfName) %in% .packages(all.available=TRUE)) ){
AnnPkg <- .cdfName2AnnPkg(cdfName)
suppressPackageStartupMessages(requireNamespace(AnnPkg,quietly=TRUE))
Try(probeset2GENENAME <- getFromNamespace(paste0(cdfName,"GENENAME"),AnnPkg))
Try(geneNames <- AnnotationDbi::mget(ls(cdfenv),envir=probeset2GENENAME))
Try(geneNames <- unlist(lapply(geneNames,function(x) paste(x,collapse="; "))))
Try(assign("geneNames",geneNames,affylmGUIenvironment))
Try(probeset2SYMBOL <- getFromNamespace(paste0(cdfName,"SYMBOL"),AnnPkg))
Try(geneSymbols <- AnnotationDbi::mget(ls(cdfenv),envir=probeset2SYMBOL))
Try(geneSymbols <- unlist(lapply(geneSymbols,function(x) paste(x,collapse="; "))))
Try(assign("geneSymbols",geneSymbols,affylmGUIenvironment))
Try(genelist <- data.frame(ID=ls(cdfenv),Symbol=geneSymbols,Name=geneNames,stringsAsFactors=FALSE))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}else{
Try(genelist <- data.frame(ID=ls(cdfenv),stringsAsFactors=FALSE))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
)
}else{
Try(genelist <- data.frame(ID=ls(cdfenv),Symbol=geneSymbols,Name=geneNames,stringsAsFactors=FALSE))
}
)
}
if(ExportTopNNToptables){
Try(
HTML.title(
paste("<a name=\"TopNNToptables\">Top ",numberOfGenes," Differentially Expressed Genes for each Contrast in Contrasts Parameterization ",
ContrastParameterizationNamesVec[contrastParameterizationIndex],"</a>",sep=""),
HR=2
)
)
Try(NormalizedAffyData.exprs <- get("NormalizedAffyData.exprs",envir=affylmGUIenvironment))
Try(if(is.null(fit$Amean)) fit$Amean <- rowMeans(NormalizedAffyData.exprs))
Try(fit$genes <- genelist)
for(coef in (1:NumContrasts)){
Try(options(digits=3))
Try(table1 <- topTable(coef=coef,number=numberOfGenes,genelist=genelist,adjust.method=adjustMethod,sort.by=sortBy,fit=fit))
Try(toptableDisplay <- rep("s",ncol(table1)+1))
Try(toptableDisplay[1] <- "d")
Try(
for (i in (2:(ncol(table1)+1))){
Try(if (colnames(table1)[i-1]=="M") toptableDisplay[i] <- "f")
Try(if (colnames(table1)[i-1]=="A") toptableDisplay[i] <- "f")
Try(if (colnames(table1)[i-1]=="t") toptableDisplay[i] <- "f")
Try(if (colnames(table1)[i-1]=="P.Value") toptableDisplay[i] <- "e")
Try(if (colnames(table1)[i-1]=="B") toptableDisplay[i] <- "f")
}
)
Try(toptableXtable <- xtable(table1,display=toptableDisplay))
Try(
HTML.title(
paste(
"Top ",
numberOfGenes,
" Differentially Expressed Genes for ",
ContrastNamesVec[coef],
" sorted by ",
sortBy,
", adjust method = ",
adjustMethod,
".",
sep=""
),
HR=3
)
)
Try(print(toptableXtable,type="html",file=fileNameWithPath,append=TRUE))
}
}
if(ExportCompleteToptables){
Try(
HTML.title(
paste("<a name=\"CompleteToptables\">Complete Tables of Genes Ranked in order of Evidence for Differential Expression for each contrast in Contrasts Parameterization ",ContrastParameterizationNamesVec[contrastParameterizationIndex],"</a>",sep=""),
HR=2
)
)
Try(NormalizedAffyData.exprs <- get("NormalizedAffyData.exprs",envir=affylmGUIenvironment))
Try(
if(!("Amean" %in% names(fit))){
fit$Amean <- rowMeans(NormalizedAffyData.exprs)
}
)
Try(fit$genes <- genelist)
for(coef in (1:NumContrasts)){
Try(options(digits=3))
Try(table1 <- topTable(coef=coef,number=nrow(genelist),genelist=genelist,adjust.method=adjustMethod,sort.by=sortBy,fit=fit))
Try(ToptableAbsoluteFilename <- paste(HTMLfilePath ,.Platform$file.sep,"CompleteToptable_Contrast",coef,".xls",sep=""))
Try(ToptableRelativeFilename <- paste(HTMLfileRelativePath ,.Platform$file.sep,"CompleteToptable_Contrast",coef,".xls",sep=""))
Try(write.table(table1,file=ToptableAbsoluteFilename,quote=FALSE,col.names=NA,sep="\t"))
Try(HTML.title(paste("Complete Table of Genes Ranked in order of Evidence for Differential Expression for ",ContrastNamesVec[coef]),HR=3))
Try(HTMLli(txt=paste("<a href=\"",ToptableRelativeFilename,"\"><b>",paste("CompleteToptable_Contrast",coef,".xls",sep=""),"</b></a>",sep="")))
}
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(HTMLhr())
Try(HTMLli(txt="This report was generated by "))
Try(HTMLli(txt=paste("affylmGUI Version",getPackageVersion("affylmGUI"),"(by James Wettenhall), using")))
Try(HTMLli(txt=paste("affy Version",getPackageVersion("affy"),"(by Rafael A. Irizarry, Laurent Gautier and Benjamin Bolstad),")))
Try(HTMLli(txt=paste("affyPLM Version",getPackageVersion("affyPLM"),"(by Benjamin Bolstad),")))
Try(HTMLli(txt=paste("limma Version",getPackageVersion("limma"),"(by Gordon Smyth),")))
Try(HTMLli(txt=paste("R2HTML Version",getPackageVersion("R2HTML"),"(by Eric Lecoutre) and ")))
Try(HTMLli(txt=paste("xtable Version",getPackageVersion("xtable"),"(by David Dahl)")))
Try(HTMLEndFile())
invisible()
}
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affylmGUI documentation built on Nov. 8, 2020, 11 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions ExportHTMLreport GetComponentsToExportInHTMLreport HTMLplotUsingFunction
Documented in ExportHTMLreport GetComponentsToExportInHTMLreport HTMLplotUsingFunction
HTMLplotUsingFunction <- function(
Caption = "",
File = "plot.html",
GraphRelativeDirectory = ".",
GraphAbsoluteDirectory = NULL,
GraphFileName = "",
GraphSaveAs = "png",
GraphBorder = 1,
Align = "center",
plotFunction = NULL,
Width=600,
Height=600,
PointSize=12,
BG="white",
res=72,
...)
# R2HTML::HTMLplot function modified to accept a plotFunction argument, rather than using the main R Graphics Device.
{
if(is.null(GraphAbsoluteDirectory)){
GraphAbsoluteDirectory <- getwd()
#For eg. "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files"
}
if(GraphFileName == ""){
nowd <- date() #For eg. = "Thu Sep 20 11:27:14 2007"
# 000000000111111111122222
# 123456789012345678901234
GraphFileName <- paste(
"GRAPH_",
substring(nowd, 5, 7),
substring(nowd, 9, 10), "_",
substring(nowd, 12, 13),
substring(nowd, 15, 16),
substring(nowd, 18, 19),
sep = ""
)
# Example name = GRAPH_Sep20_112714
}
GraphFileName <- paste(GraphFileName, GraphSaveAs, sep=".")
# for eg. = GRAPH_Sep20_112714.png
#AbsGraphFileName <- paste(GraphRelativeDirectory,.Platform$file.sep,GraphFileName,sep="")
AbsGraphFileName <- file.path(GraphAbsoluteDirectory, GraphFileName)
#For eg. = "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/GRAPH_Sep20_112714.png"
if(GraphSaveAs=="png"){
if(is.null(plotFunction)){
dev.print(png, file = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG)
}else{
Try( #if it is linux like
if(exists("X11", envir=.GlobalEnv) && Sys.info()["sysname"] != "Windows" && Sys.info()["sysname"] != "Darwin"){
Try(bitmap(file = AbsGraphFileName,bg=BG,res=res))
}else{ #it is MS Windows or Mac
Try(png(filename = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG))
}
)
plotFunction()
dev.off()
}
}else if (GraphSaveAs=="jpg"){
if (is.null(plotFunction)){
dev.print(jpeg, file = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG)
}else{
Try( #if it is linux like
if (exists("X11", envir=.GlobalEnv) && Sys.info()["sysname"] != "Windows" && Sys.info()["sysname"] != "Darwin"){
Try(bitmap(filename = AbsGraphFileName,bg=BG,res=res,type="jpeg"))
}else{ #it is MS Windows or Mac
Try(jpeg(filename = AbsGraphFileName, width=Width,height=Height,pointsize=PointSize,bg=BG))
}
)
plotFunction()
dev.off()
}
}else{
stop("GraphSaveAs must be either jpg, or png")
}
cat(
paste(
"<p align=",
Align,
"><img src='",
paste(GraphRelativeDirectory,"/",GraphFileName,sep=""),
"' border=",
GraphBorder,
">",
sep = "",
collapse = ""
),
file = File,
append = TRUE,
sep = ""
)
if (Caption != "") {
cat(paste("<br><i>", Caption, "</i>"), file = File, append = TRUE, sep = "")
}
cat("</P>", file = File, append = TRUE, sep = "\n")
if (exists("HTMLenv",where=".GlobalEnv",mode="environment")){
try(assign(".HTML.graph", TRUE, envir = get("HTMLenv", envir = .GlobalEnv)))
}
###try(assign(".HTML.graph", TRUE, envir = get("HTMLenv", envir = .GlobalEnv)))
invisible()
}
GetComponentsToExportInHTMLreport <- function(contrastParameterizationIndex=NULL)
# Get numberOfGenes, adjustMethod and sortBy from environment if they are available.
# Otherwise set them to default values.
{
Try(
if(exists("numberOfGenes",envir=affylmGUIenvironment)){
Try(numberOfGenes <- get("numberOfGenes",envir=affylmGUIenvironment))
if(numberOfGenes > 100)numberOfGenes <- 100 #dontplot more than 100 here
}else{
Try(numberOfGenes <- 50)
Try(assign("numberOfGenes",numberOfGenes,affylmGUIenvironment))
}
)
Try(
if(exists("sortBy",envir=affylmGUIenvironment)){
Try(sortBy <- get("sortBy",envir=affylmGUIenvironment))
}else{
Try(sortBy <- "B")
Try(assign("sortBy",sortBy,affylmGUIenvironment))
}
)
Try(
if(exists("adjustMethod",envir=affylmGUIenvironment)){
Try(adjustMethod <- get("adjustMethod",envir=affylmGUIenvironment))
}else{
Try(adjustMethod <- "BH")
Try(assign("adjustMethod",adjustMethod,affylmGUIenvironment))
}
)
Try(NumContrastParameterizations <- get("NumContrastParameterizations",envir=affylmGUIenvironment))
Try(ttHTMLreportDialog<-tktoplevel(.affylmGUIglobals$ttMain))
Try(tkwm.deiconify(ttHTMLreportDialog))
Sys.sleep(0.1)
Try(tkgrab.set(ttHTMLreportDialog))
Try(tkfocus(ttHTMLreportDialog))
Try(tkwm.title(ttHTMLreportDialog,"HTML Report"))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),tklabel(ttHTMLreportDialog,text=" ")))
Try(TargetsTcl <- tclVar("1"))
Try(NormalizationMethodTcl <- tclVar("1"))
Try(RawIntensityBoxPlotTcl <- tclVar("1"))
Try(NormalizedIntensityBoxPlotTcl <- tclVar("1"))
Try(DesignMatrixTcl <- tclVar("1"))
#set ContrastMatrixTcl
Try(
if (NumContrastParameterizations>0)
Try(ContrastMatrixTcl <- tclVar("1"))
else
Try(ContrastMatrixTcl <- tclVar("0"))
)
#set MAPlotsContrastsTcl
Try(
if (NumContrastParameterizations>0)
Try(MAPlotsContrastsTcl <- tclVar("1"))
else
Try(MAPlotsContrastsTcl <- tclVar("0"))
)
#set TopNNToptablesTcl
Try(
if (NumContrastParameterizations>0)
Try(TopNNToptablesTcl <- tclVar("1"))
else
Try(TopNNToptablesTcl <- tclVar("0"))
)
#set CompleteToptablesTcl
Try(
if (NumContrastParameterizations>0)
Try(CompleteToptablesTcl <- tclVar("1"))
else
Try(CompleteToptablesTcl <- tclVar("0"))
)
#set TopNNToptablesTcl
Try(
if (NumContrastParameterizations>0)
Try(TopNNToptablesTcl <- tclVar("1"))
else
Try(TopNNToptablesTcl <- tclVar("0"))
)
#set CompleteToptablesTcl
Try(CompleteToptablesTcl <- tclVar("0"))
Try(TargetsCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=TargetsTcl))
Try(NormalizationMethodCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=NormalizationMethodTcl))
Try(RawIntensityBoxPlotCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=RawIntensityBoxPlotTcl))
Try(NormalizedIntensityBoxPlotCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=NormalizedIntensityBoxPlotTcl))
Try(DesignMatrixCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=DesignMatrixTcl))
Try(ContrastMatrixCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=ContrastMatrixTcl))
Try(MAPlotsContrastsCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=MAPlotsContrastsTcl))
Try(TopNNToptablesCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=TopNNToptablesTcl))
Try(CompleteToptablesCheckbox <- tkcheckbutton(ttHTMLreportDialog,variable=CompleteToptablesTcl))
Try(lbl2 <- tklabel(ttHTMLreportDialog,text="Components to be Included in the HTML Report",font=.affylmGUIglobals$affylmGUIfont2))
tkgrid(tklabel(ttHTMLreportDialog,text=" "),lbl2)
Try(tkgrid.configure(lbl2,columnspan=3,sticky="w"))
tkgrid(tklabel(ttHTMLreportDialog,text=" "))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="RNA Targets",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),TargetsCheckbox,currentLabel))
Try(tkgrid.configure(TargetsCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Normalization Method",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),NormalizationMethodCheckbox,currentLabel))
Try(tkgrid.configure(NormalizationMethodCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Raw Intensity Box Plot",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),RawIntensityBoxPlotCheckbox,currentLabel))
Try(tkgrid.configure(RawIntensityBoxPlotCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Normalized Intensity Box Plot",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),NormalizedIntensityBoxPlotCheckbox,currentLabel))
Try(tkgrid.configure(NormalizedIntensityBoxPlotCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Design Matrix (Parameterization)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),DesignMatrixCheckbox,currentLabel))
Try(tkgrid.configure(DesignMatrixCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Contrasts Matrix (Parameterization)",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),ContrastMatrixCheckbox,currentLabel))
Try(tkgrid.configure(ContrastMatrixCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="M A Plots for Contrasts",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),MAPlotsContrastsCheckbox,currentLabel))
Try(tkgrid.configure(MAPlotsContrastsCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text=paste("Top ",numberOfGenes," DE Genes. TopTable sets Adjust Method = ",adjustMethod," sort by = ",sortBy,".",sep=""),font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),TopNNToptablesCheckbox,currentLabel))
Try(tkgrid.configure(TopNNToptablesCheckbox,sticky="e")); Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
Try(currentLabel <- tklabel(ttHTMLreportDialog,text="Complete Lists of DE-Ranked Genes",font=.affylmGUIglobals$affylmGUIfont2))
Try(tkgrid(tklabel(ttHTMLreportDialog,text=" "),CompleteToptablesCheckbox,currentLabel))
Try(tkgrid.configure(CompleteToptablesCheckbox,sticky="e"));
Try(tkgrid.configure(currentLabel,sticky="w",columnspan=2))
if (NumContrastParameterizations==0){
Try(tkconfigure(ContrastMatrixCheckbox, state="disabled"))
Try(tkconfigure(MAPlotsContrastsCheckbox, state="disabled"))
Try(tkconfigure(TopNNToptablesCheckbox, state="disabled"))
Try(tkconfigure(CompleteToptablesCheckbox,state="disabled"))
}
tkgrid(tklabel(ttHTMLreportDialog,text=" "))
tkgrid(tklabel(ttHTMLreportDialog,text=" "))
ReturnVal <- list()
onOK <- function(){
if (tclvalue(TargetsTcl) =="1") ReturnVal[["Targets"]] <- TRUE else ReturnVal[["Targets"]] <- FALSE
if (tclvalue(NormalizationMethodTcl) =="1") ReturnVal[["NormalizationMethod"]] <- TRUE else ReturnVal[["NormalizationMethod"]] <- FALSE
if (tclvalue(RawIntensityBoxPlotTcl) =="1") ReturnVal[["RawIntensityBoxPlot"]] <- TRUE else ReturnVal[["RawIntensityBoxPlot"]] <- FALSE
if (tclvalue(NormalizedIntensityBoxPlotTcl)=="1") ReturnVal[["NormalizedIntensityBoxPlot"]] <- TRUE else ReturnVal[["NormalizedIntensityBoxPlot"]] <- FALSE
if (tclvalue(DesignMatrixTcl) =="1") ReturnVal[["DesignMatrix"]] <- TRUE else ReturnVal[["DesignMatrix"]] <- FALSE
if (tclvalue(ContrastMatrixTcl) =="1") ReturnVal[["ContrastsMatrix"]] <- TRUE else ReturnVal[["ContrastsMatrix"]] <- FALSE
if (tclvalue(MAPlotsContrastsTcl) =="1") ReturnVal[["MAPlotsContrasts"]] <- TRUE else ReturnVal[["MAPlotsContrasts"]] <- FALSE
if (tclvalue(TopNNToptablesTcl) =="1") ReturnVal[["TopNNToptablesTcl"]] <- TRUE else ReturnVal[["TopNNToptables"]] <- FALSE
if (tclvalue(CompleteToptablesTcl) =="1") ReturnVal[["CompleteToptablesTcl"]] <- TRUE else ReturnVal[["CompleteToptablesTcl"]] <- FALSE
Try(tkgrab.release(ttHTMLreportDialog));
Try(tkdestroy(ttHTMLreportDialog));
Try(tkfocus(.affylmGUIglobals$ttMain))
ReturnVal <<- ReturnVal
}
onCancel <- function(){
Try(tkgrab.release (ttHTMLreportDialog));
Try(tkdestroy (ttHTMLreportDialog));
Try(tkfocus (.affylmGUIglobals$ttMain));
ReturnVal <<- list()
}
OK.but <-tkbutton(ttHTMLreportDialog,text=" OK ",command=onOK, font=.affylmGUIglobals$affylmGUIfont2)
Cancel.but <-tkbutton(ttHTMLreportDialog,text=" Cancel ",command=onCancel,font=.affylmGUIglobals$affylmGUIfont2)
tkgrid(tklabel(ttHTMLreportDialog,text=" "),tklabel(ttHTMLreportDialog,text=" "),OK.but,Cancel.but,tklabel(ttHTMLreportDialog,text=" "),tklabel(ttHTMLreportDialog,text=" "))
tkgrid.configure(OK.but, sticky="e")
tkgrid.configure(Cancel.but,sticky="w")
tkgrid(
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" "),
tklabel(ttHTMLreportDialog,text=" ")
)
Try(tkfocus(ttHTMLreportDialog))
Try(tkbind(ttHTMLreportDialog, "<Destroy>", function() {Try(tkgrab.release(ttHTMLreportDialog));Try(tkfocus(.affylmGUIglobals$ttMain));}))
Try(tkwait.window(ttHTMLreportDialog))
return (ReturnVal)
}
ExportHTMLreport <- function(){
# We will use the R2HTML package, but with my own HTMLplot function.
# Will we need xtable or does R2HTML have its own HTMLtable function?
#get numberOfGenes,adjustMethod and sortBy from environment if they are available, if not, set them to default values
Try(
if(exists("numberOfGenes",envir=affylmGUIenvironment)){
Try(numberOfGenes <- get("numberOfGenes",envir=affylmGUIenvironment))
if(numberOfGenes > 100)numberOfGenes <- 100 #dontplot more than 100 here
}else{
Try(numberOfGenes <- 50)
Try(assign("numberOfGenes",numberOfGenes,affylmGUIenvironment))
}
)
Try(
if(exists("sortBy",envir=affylmGUIenvironment)){
Try(sortBy <- get("sortBy",envir=affylmGUIenvironment))
}else{
Try(sortBy <- "B")
Try(assign("sortBy",sortBy,affylmGUIenvironment))
}
)
Try(
if(exists("adjustMethod",envir=affylmGUIenvironment)){
Try(adjustMethod <- get("adjustMethod",envir=affylmGUIenvironment))
}else{
Try(adjustMethod <- "BH")
Try(assign("adjustMethod",adjustMethod,affylmGUIenvironment))
}
)
Try(limmaDataSetNameText <- get("limmaDataSetNameText" ,envir=affylmGUIenvironment)) #for eg: [1] "alg_Est_gcrma_3C"
Try(ArraysLoaded <- get("ArraysLoaded" , envir=affylmGUIenvironment))
Try(NumContrastParameterizations <- get("NumContrastParameterizations" ,envir=affylmGUIenvironment)) #for eg: [1] 1
Try(ContrastParameterizationList <- get("ContrastParameterizationList" ,envir=affylmGUIenvironment))
# for eg:
#> summary(ContrastParameterizationList)
# Length Class Mode
#ContrastParameterizationName.1 5 -none- list
#ContrastParameterizationList is a list with entrys for each gene(?) for:
#some values for each gene off the top of the screen, followed by all of this data:
#$ContrastParameterizationName.1$eb$rank
#[1] 4
#$ContrastParameterizationName.1$eb$assign
#NULL
#$ContrastParameterizationName.1$eb$qr
#$qr
# EstAbsent10 EstAbsent48 EstPresent10 EstPresent48
#low10-1.cel -1.4142136 0.0000000 0.0000000 0.0000000
#low10-2.cel 0.7071068 -1.4142136 0.0000000 0.0000000
#high10-1.cel 0.0000000 0.0000000 -1.4142136 0.0000000
#high10-2.cel 0.0000000 0.0000000 0.7071068 -1.4142136
#low48-1.cel 0.0000000 0.7071068 0.0000000 0.0000000
#low48-2.cel 0.0000000 0.7071068 0.0000000 0.0000000
#high48-1.cel 0.0000000 0.0000000 0.0000000 0.7071068
#high48-2.cel 0.0000000 0.0000000 0.0000000 0.7071068
#$qraux
#[1] 1.707107 1.000000 1.707107 1.000000
#$pivot
#[1] 1 2 3 4
#$tol
#[1] 1e-07
#$rank
#[1] 4
#attr(,"class")
#[1] "qr"
#$ContrastParameterizationName.1$eb$df.residual
# [1] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
# [85] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
# ... ...................................
#[12601] 4 4 4 ...
#$ContrastParameterizationName.1$eb$sigma
# 100_g_at 1000_at 1001_at 1002_f_at 1003_s_at 1004_at
# 0.210371658 0.229581752 0.056224969 0.079154826 0.035168585 0.062620730
# 1005_at 1006_at 1007_s_at 1008_f_at 1009_at 101_at
# ... ... ... ... ... ...
#$ContrastParameterizationName.1$eb$cov.coefficients
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#(EstAbsent10)-(EstAbsent48) 1.0 0.0 0.5
#(EstPresent10)-(EstPresent48) 0.0 1.0 0.5
#(EstAbsent10)-(EstPresent48) 0.5 0.5 1.0
#$ContrastParameterizationName.1$eb$stdev.unscaled
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#100_g_at 1 1 1
#1000_at 1 1 1
# ... ... ... ...
#$ContrastParameterizationName.1$eb$contrasts
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#EstAbsent10 1 0 1
#EstAbsent48 -1 0 0
#EstPresent10 0 1 0
#EstPresent48 0 -1 -1
#$ContrastParameterizationName.1$eb$df.prior
#[1] 1.916164
#$ContrastParameterizationName.1$eb$s2.prior
#[1] 0.01619520
#$ContrastParameterizationName.1$eb$var.prior
#[1] 156.9730 123.4235 256.8846
#$ContrastParameterizationName.1$eb$proportion
#[1] 0.01
#$ContrastParameterizationName.1$eb$s2.post
# 100_g_at 1000_at 1001_at 1002_f_at 1003_s_at 1004_at
# 0.035167654 0.040881861 0.007382765 0.009481584 0.006081640 0.007896685
# 1005_at 1006_at 1007_s_at 1008_f_at 1009_at 101_at
# 0.031434553 0.009843242 0.042246541 0.501898805 0.061243025 0.008799333
# ... ... ... ... ... ...
#AND
#$ContrastParameterizationName.1$eb$t
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#100_g_at 1.030421e+00 -8.576221e-01 1.325653e+00
#1000_at -7.997174e-01 -2.053407e+00 6.645345e-02
# ... ... ...
# AND
#$ContrastParameterizationName.1$eb$p.value
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#100_g_at 3.430840e-01 4.244753e-01 2.338416e-01
#1000_at 4.547765e-01 8.650180e-02 9.492055e-01
# ... ... ...
#AND
#$ContrastParameterizationName.1$eb$lods
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
# ... ... ...
#AND
#$ContrastParameterizationName.1$contrastsMatrixInList
#$ContrastParameterizationName.1$contrastsMatrixInList$contrasts
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#EstAbsent10 1 0 1
#EstAbsent48 -1 0 0
#EstPresent10 0 1 0
#EstPresent48 0 -1 -1
#$ContrastParameterizationName.1$contrastsMatrixInList$contrastsCreatedFromDropDowns
#[1] TRUE
#$ContrastParameterizationName.1$contrastsMatrixInList$Param1
#[1] 1 3 1
#$ContrastParameterizationName.1$contrastsMatrixInList$Param2
#[1] 2 4 4
#$ContrastParameterizationName.1$ContrastParameterizationNameText
#[1] "ContSet1"
Try(ContrastParameterizationTREEIndexVec <- get("ContrastParameterizationTREEIndexVec",envir=affylmGUIenvironment)) #for eg: [1] 1
if(ArraysLoaded==FALSE){
Try(tkmessageBox(title="Export HTML Report",message="No arrays have been loaded. Please try New or Open from the File menu.",type="ok",icon="error"))
Try(tkfocus(.affylmGUIglobals$ttMain))
return()
}
if(NumContrastParameterizations>0){
#Select which parameterization
Try(contrastParameterizationIndex <- ChooseContrastParameterization()) #for eg: [1] 1
#If click cancel button, then exit this routine
Try(if (contrastParameterizationIndex==0) return()) # Cancel
Try(ContrastParameterizationNamesVec <- get("ContrastParameterizationNamesVec",envir=affylmGUIenvironment)) #for eg: [1] "ContSet1"
#store locally TREEindex for chosen parameterization
Try(.affylmGUIglobals$ContrastParameterizationTREEIndex <- ContrastParameterizationTREEIndexVec[contrastParameterizationIndex]) #for eg: [1] 1
#setup contrast matrix
Try(contrastsMatrix <- as.matrix(ContrastParameterizationList[[contrastParameterizationIndex]]$contrastsMatrixInList$contrasts))
# (EstAbsent10)-(EstAbsent48) (EstPresent10)-(EstPresent48) (EstAbsent10)-(EstPresent48)
#EstAbsent10 1 0 1
#EstAbsent48 -1 0 0
#EstPresent10 0 1 0
#EstPresent48 0 -1 -1
#>
#get vector of names for contrasts
Try(ContrastNamesVec <- colnames(contrastsMatrix))
#for eg: [1] "(EstAbsent10)-(EstAbsent48)" "(EstPresent10)-(EstPresent48)" "(EstAbsent10)-(EstPresent48)"
Try(NumContrasts <- length(ContrastNamesVec)) #for eg: 3
Try(ContrastParameterizationNameNode <- paste("ContrastParameterizationName.",.affylmGUIglobals$ContrastParameterizationTREEIndex,sep=""))
#for eg: "ContrastParameterizationName.1"
Try(fit <- (ContrastParameterizationList[[ContrastParameterizationNameNode]])$fit)
#> summary(fit)
# Length Class Mode
#coefficients 37875 -none- numeric
#rank 1 -none- numeric
#assign 0 -none- NULL
#qr 5 qr list
#df.residual 12625 -none- numeric
#sigma 12625 -none- numeric
#cov.coefficients 9 -none- numeric
#stdev.unscaled 37875 -none- numeric
#contrasts 12 -none- numeric
#Amean 12625 -none- numeric
Try(fit <- eBayes(fit))
#> summary(fit)
# Length Class Mode
#coefficients 37875 -none- numeric
#rank 1 -none- numeric
#assign 0 -none- NULL
#qr 5 qr list
#df.residual 12625 -none- numeric
#sigma 12625 -none- numeric
#cov.coefficients 9 -none- numeric
#stdev.unscaled 37875 -none- numeric
#contrasts 12 -none- numeric
#Amean 12625 -none- numeric
#df.prior 1 -none- numeric
#s2.prior 1 -none- numeric
#var.prior 3 -none- numeric
#proportion 1 -none- numeric
#s2.post 12625 -none- numeric
#t 37875 -none- numeric
#p.value 37875 -none- numeric
#lods 37875 -none- numeric
Try(ComponentsToExport <- GetComponentsToExportInHTMLreport(contrastParameterizationIndex))
}else{
Try(ComponentsToExport <- GetComponentsToExportInHTMLreport())
}
#if nothing selected, exit this routine
Try(if (length(ComponentsToExport)==0) return())
#Setup files to use for HTML report
Try(fileNameWithPath<- tkgetSaveFile(initialfile=limmaDataSetNameText,filetypes="{{HTML Files} {.html .htm}} {{All files} *}"))
#for eg: W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C
#Try(tkmessageBox(title="229:affylmGUI-htmlreport",message=paste("fileNameWithPath =",fileNameWithPath),icon="info",default="ok"))
#if null filename selected, exit this routine
Try(if (nchar(tclvalue(fileNameWithPath))==0)return())
Try(path <- tclvalue(tclfile.dir (tclvalue(fileNameWithPath)))) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files"
#Try(tkmessageBox(title="235:affylmGUI-htmlreport",message=paste("path =",path),icon="info",default="ok"))
Try(fileName <- tclvalue(tclfile.tail(tclvalue(fileNameWithPath)))) #for eg: "alg_Est_gcrma_3C"
#Try(tkmessageBox(title="242:affylmGUI-htmlreport",message=paste("fileName =",fileName),icon="info",default="ok"))
Try(len <- nchar(fileName))
if (len<4){
Try(fileName <- paste(fileName,".html",sep=""))
}else if((tolower(substring(fileName,len-4,len))!=".html") &&(len<5 || (tolower(substring(fileName,len-4,len))!=".html"))){
Try(fileName <- paste(fileName,".html",sep="")) #for eg: "alg_Est_gcrma_3C.html"
}
Try(fileNameWithoutExtension <- substring(fileName,1,nchar(fileName)-5)) #for eg: "alg_Est_gcrma_3C"
Try(HTMLfilePath <- paste(path,.Platform$file.sep,fileNameWithoutExtension,"_files",sep="")) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C_files"
Try(HTMLfileRelativePath <- paste(fileNameWithoutExtension,"_files",sep="")) #for eg: "alg_Est_gcrma_3C_files"
Try(dir.create(HTMLfilePath))
Try(fileNameWithPath <- paste(path,"/",fileName,sep="")) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C.html"
Try(R2HTMLpath <- system.file(package="R2HTML","output")) #for eg: [1] "C:/R/R-2.6.0alpha/library/R2HTML/output"
Try(cssFileSource <- paste(R2HTMLpath,"/","R2HTML.css",sep="")) #for eg: [1] "C:/R/R-2.6.0alpha/library/R2HTML/output/R2HTML.css"
Try(cssFileDestination <- paste(path,"/","R2HTML.css",sep="")) #for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/R2HTML.css"
Try(R2HTMLlogoSource <- paste(R2HTMLpath,"/","R2HTMLlogo.png",sep="")) #for eg: [1] "C:/R/R-2.6.0alpha/library/R2HTML/output/R2HTMLlogo.png"
Try(R2HTMLlogoDestination <- paste(path,"/","R2HTMLlogo.png",sep="")) #for eg: [1] "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/R2HTMLlogo.png"
Try(file.copy(cssFileSource,cssFileDestination,overwrite=TRUE)) #for eg: TRUE
Try(file.copy(R2HTMLlogoSource,R2HTMLlogoDestination,overwrite=TRUE)) #for eg: TRUE
Try(HTMLtarget <- HTMLInitFile(path,filename=fileNameWithoutExtension,Title=paste(limmaDataSetNameText,"- Statistical Microarray Analysis using affylmGUI"), HTMLframe=FALSE,BackGroundColor="#FFFFFF"))
# for eg: "W:/aaa-R/eg_datasets/Affy-Estrogen_Data/estrogen_CEL_files/alg_Est_gcrma_3C.html"
# The following is written to this file:
# <html xmlns:mml="http://www.w3.org/1998/Math/MathML">
# <head>
# <title> alg_Est_gcrma_3C - Statistical Microarray Analysis using affylmGUI </title>
# <link rel=stylesheet href="R2HTML.css" type=text/css>
# <object id="mathplayer" classid="clsid:32F66A20-7614-11D4-BD11-00104BD3F987"></object>
# <?import namespace="mml" implementation="#mathplayer"?>
# <script type="text/javascript" src="ASCIIMathML.js"></script>
# <link href="./runtime/styles/xp/grid.css" rel="stylesheet" type="text/css" ></link>
# <link href="gridR2HTML.css" rel="stylesheet" type="text/css" ></link>
# <script src="./runtime/lib/grid.js"></script>
# <script src="./gridR2HTML.js"></script>
# <script>
# nequations=0;
# </script>
# </head>
# <body onload="translate()" bgcolor= #FFFFFF background="" >
Try(HTML.title(paste(limmaDataSetNameText,"- Statistical Microarray Analysis using affylmGUI"),HR=1)) #for eg: NULL
# for eg: written to html file is:
# <h1 > alg_Est_gcrma_3C - Statistical Microarray Analysis using affylmGUI</h1>
Try(ExportTargets <- ComponentsToExport$Targets)
Try(ExportNormalizationMethod <- ComponentsToExport$NormalizationMethod)
Try(ExportRawIntensityBoxPlot <- ComponentsToExport$RawIntensityBoxPlot)
Try(ExportNormalizedIntensityBoxPlot <- ComponentsToExport$NormalizedIntensityBoxPlot)
Try(ExportDesignMatrix <- ComponentsToExport$DesignMatrix)
Try(ExportContrastsMatrix <- ComponentsToExport$ContrastsMatrix)
Try(ExportMAPlotsContrasts <- ComponentsToExport$MAPlotsContrasts)
Try(ExportTopNNToptables <- ComponentsToExport$TopNNToptables)
Try(ExportCompleteToptables <- ComponentsToExport$CompleteToptables)
#All the above are set to TRUE or FALSE, depending on what was chosen in the dialogue box
#This sets up parameters for the plots
if(ExportRawIntensityBoxPlot || ExportNormalizedIntensityBoxPlot || ExportMAPlotsContrasts){
Try(
#if linux like
if (exists("X11", envir=.GlobalEnv) && Sys.info()["sysname"] != "Windows" && Sys.info()["sysname"] != "Darwin"){
Try(pngParams <- GetJpegOrPngX11Params(graphFileType="PNG")) #sets background colour(bg) and resolution(res)
Try(if (length(pngParams)==0) return())
Try(plotBG <- pngParams$bg)
Try(plotRes <- pngParams$res)
}else{
#if Windows or Mac
Try(pngParams <- GetJpegOrPngParams(graphFileType="PNG")) #sets width, height, background colour(bg) and Font Size(pointsize)
Try(if (length(pngParams)==0) return())
Try(plotWidth <- pngParams$width)
Try(plotHeight <- pngParams$height)
Try(plotPointSize <- pngParams$pointsize)
Try(plotBG <- pngParams$bg)
}
)
}
Try(HTML.title("Contents",HR=2)) # this writes " <h2 > Contents</h2>" to html file
#This writes links to html file for each feature selected
Try(if (ExportTargets) Try(HTMLli(txt="<a href=\"#Targets\"><b>Targets</b></a>")))
Try(if (ExportNormalizationMethod) Try(HTMLli(txt="<a href=\"#NormalizationMethod\"><b>Normalization Method</b></a>")))
Try(if (ExportRawIntensityBoxPlot) Try(HTMLli(txt="<a href=\"#RawIntensityBoxPlot\"><b>Raw Intensity Box Plot</b></a>")))
Try(if (ExportNormalizedIntensityBoxPlot) Try(HTMLli(txt="<a href=\"#NormalizedIntensityBoxPlot\"><b>Normalized Intensity Box Plot</b></a>")))
Try(if (ExportDesignMatrix) Try(HTMLli(txt="<a href=\"#DesignMatrix\"><b>Design Matrix</b></a>")))
Try(if (ExportContrastsMatrix) Try(HTMLli(txt="<a href=\"#ContrastsMatrix\"><b>Contrasts Matrix</b></a>")))
Try(if (ExportMAPlotsContrasts) Try(HTMLli(txt="<a href=\"#MAPlotsContrasts\"><b>M A Plots for Contrasts</b></a>")))
Try(if (ExportTopNNToptables) Try(HTMLli(txt=paste("<a href=\"#TopNNToptables\"><b>Tables of Top ",numberOfGenes," Differentially Expressed Genes</b></a>",sep=""))))
Try(if (ExportCompleteToptables) Try(HTMLli(txt="<a href=\"#CompleteToptables\"><b>Complete Tables of Genes Ranked in order of Evidence for Differential Expression</b></a>")))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(tkfocus(.affylmGUIglobals$ttMain))
if (ExportTargets){
Try(Targets <- get("Targets",envir=affylmGUIenvironment))
#for eg: Targets is:
# Name FileName Target
#1 Abs10.1 low10-1.cel EstAbsent10
#2 Abs10.2 low10-2.cel EstAbsent10
#3 Pres10.1 high10-1.cel EstPresent10
#4 Pres10.2 high10-2.cel EstPresent10
#5 Abs48.1 low48-1.cel EstAbsent48
#6 Abs48.2 low48-2.cel EstAbsent48
#7 Pres48.1 high48-1.cel EstPresent48
#8 Pres48.2 high48-2.cel EstPresent48
Try(displayVector <- rep("s",ncol(Targets)+1)) #for eg: [1] "s" "s" "s" "s"
Try(
for (i in (0:ncol(Targets))){
if (i==0 || colnames(Targets)[i]=="SlideNumber"){
displayVector[i] <- "d"
}
}
)
#for eg: This has set the displayVector to [1] "s" "s" "s" "s"
Try(TargetsXtable <- xtable(Targets,display=displayVector))
# for eg: This outputs:
# % latex table generated in R 2.6.0 by xtable 1.5-1 package
# % Thu Sep 20 16:44:04 2007
# \begin{table}[ht]
# \begin{center}
# \begin{tabular}{rlll}
# \hline
# & Name & FileName & Target \\
# \hline
# 1 & Abs10.1 & low10-1.cel & EstAbsent10 \\
# 2 & Abs10.2 & low10-2.cel & EstAbsent10 \\
# 3 & Pres10.1 & high10-1.cel & EstPresent10 \\
# 4 & Pres10.2 & high10-2.cel & EstPresent10 \\
# 5 & Abs48.1 & low48-1.cel & EstAbsent48 \\
# 6 & Abs48.2 & low48-2.cel & EstAbsent48 \\
# 7 & Pres48.1 & high48-1.cel & EstPresent48 \\
# 8 & Pres48.2 & high48-2.cel & EstPresent48 \\
# \hline
# \end{tabular}
# \end{center}
# \end{table}
Try(HTML.title("<a name=\"Targets\">RNA Targets</a>",HR=2)) #for eg: this writes " <h2 > <a name="Targets">RNA Targets</a></h2>" to html file
Try(print(TargetsXtable,type="html",file=fileNameWithPath,append=TRUE))
#For eg: This prints the following to the html file:
# <!-- Thu Sep 20 16:46:24 2007 -->
# <TABLE border=1>
# <TR> <TH> </TH> <TH> Name </TH> <TH> FileName </TH> <TH> Target </TH> </TR>
# <TR> <TD align="right"> 1 </TD> <TD> Abs10.1 </TD> <TD> low10-1.cel </TD> <TD> EstAbsent10 </TD> </TR>
# <TR> <TD align="right"> 2 </TD> <TD> Abs10.2 </TD> <TD> low10-2.cel </TD> <TD> EstAbsent10 </TD> </TR>
# <TR> <TD align="right"> 3 </TD> <TD> Pres10.1 </TD> <TD> high10-1.cel </TD> <TD> EstPresent10 </TD> </TR>
# <TR> <TD align="right"> 4 </TD> <TD> Pres10.2 </TD> <TD> high10-2.cel </TD> <TD> EstPresent10 </TD> </TR>
# <TR> <TD align="right"> 5 </TD> <TD> Abs48.1 </TD> <TD> low48-1.cel </TD> <TD> EstAbsent48 </TD> </TR>
# <TR> <TD align="right"> 6 </TD> <TD> Abs48.2 </TD> <TD> low48-2.cel </TD> <TD> EstAbsent48 </TD> </TR>
# <TR> <TD align="right"> 7 </TD> <TD> Pres48.1 </TD> <TD> high48-1.cel </TD> <TD> EstPresent48 </TD> </TR>
# <TR> <TD align="right"> 8 </TD> <TD> Pres48.2 </TD> <TD> high48-2.cel </TD> <TD> EstPresent48 </TD> </TR>
# </TABLE>
# <!-- html table generated in R 2.6.0 by xtable 1.5-1 package -->
}
if (ExportNormalizationMethod){
Try(NormMethod <- get("NormMethod", envir=affylmGUIenvironment)) #for eg: GCRMA
Try(HTML.title("<a name=\"NormalizationMethod\">Normalization method</a>",HR=2)) #writes to html: " <h2 > <a name="NormalizationMethod">Normalization method</a></h2>"
Try(
if(NormMethod=="RMA"){
Try(HTMLli(txt="<b>RMA (Robust Multiarray Averaging)</b>"))
}else if(NormMethod=="PLM"){
Try(HTMLli(txt="<b>PLM (Robust Probe-level Linear Model)</b>"))
}else if(NormMethod=="GCRMA"){
Try(HTMLli(txt="<b>GCRMA (GC Robust Multiarray Averaging)</b>"))
}else{
Try(HTMLli(txt="<b>UnKnown (Unrecognised method - check with package maintainer)</b>"))
}
) #which writes to the html file for eg: "<br><li><b>GCRMA (GC Robust Multiarray Averaging)</b>"
}
if(ExportRawIntensityBoxPlot){
Try(HTML.title("<a name=\"RawIntensityBoxPlot\">Raw (Unnormalized) Intensity Box Plot</a>",HR=2))
#which writes for eg: <h2 > <a name="RawIntensityBoxPlot">Raw (Unnormalized) Intensity Box Plot</a></h2>
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
#for eg: this is:
#AffyBatch object
#size of arrays=640x640 features (8 kb)
#cdf=HG_U95Av2 (12625 affyids)
#number of samples=8
#number of genes=12625
#annotation=hgu95av2
#notes=
Try(SlideNamesVec <- get("SlideNamesVec",envir=affylmGUIenvironment)) #for eg: [1] "Abs10.1" "Abs10.2" "Pres10.1" "Pres10.2" "Abs48.1" "Abs48.2" "Pres48.1" "Pres48.2"
#This plotFunction creates a boxplot from the raw data
Try(
plotFunction <- function(){
Try(opar<-par(bg="white",cex=0.7))
Try(boxplot(RawAffyData,col="red",las=2,names=SlideNamesVec))
Try(title(plotTitle))
Try(tmp<-par(opar))
}
)
Try(plotTitle <- "Raw intensity distribution for each slide")
Try(
HTMLplotUsingFunction(
Caption = plotTitle,
File = fileNameWithPath,
GraphRelativeDirectory = HTMLfileRelativePath ,
GraphAbsoluteDirectory = HTMLfilePath,
GraphFileName = "RawIntensityBoxPlot",
GraphSaveAs = "png",
GraphBorder = 1,
Align = "left",
plotFunction = plotFunction,
Width = plotWidth,
Height = plotHeight,
PointSize = plotPointSize,
BG = plotBG,
res = plotRes
)
)
#For eg: This writes to the html file:
# <p align=left><img src='alg_Est_gcrma_3C_files/RawIntensityBoxPlot.png' border=1><br><i> Raw intensity distribution for each slide </i></P>
#and creates a file "RawIntensityBoxPlot.png" in the "alg_Est_gcrma_3C_files" subdirectory.
}
if(ExportNormalizedIntensityBoxPlot){
Try(HTML.title("<a name=\"NormalizedIntensityBoxPlot\">Normalized Intensity Box Plot</a>",HR=2))
# for eg: this writes to the HTML file:
# <h2 > <a name="NormalizedIntensityBoxPlot">Normalized Intensity Box Plot</a></h2>
Try(NormalizedAffyData.exprs <- get("NormalizedAffyData.exprs",envir=affylmGUIenvironment))
#For eg: this is the normalized data:
#> summary(NormalizedAffyData.exprs)
# low10-1.cel low10-2.cel high10-1.cel high10-2.cel low48-1.cel low48-2.cel high48-1.cel high48-2.cel
# Min. :-0.3586 Min. :-0.3778 Min. :-0.2799 Min. :-0.2883 Min. :-0.3431 Min. :-0.3487 Min. :-0.3648 Min. :-0.3192
# 1st Qu.: 2.8701 1st Qu.: 2.8529 1st Qu.: 3.0408 1st Qu.: 3.1354 1st Qu.: 2.8521 1st Qu.: 2.9442 1st Qu.: 2.8054 1st Qu.: 2.9633
# Median : 4.0612 Median : 4.0319 Median : 4.1881 Median : 4.2567 Median : 3.9914 Median : 4.0573 Median : 3.9331 Median : 4.0457
# Mean : 5.1289 Mean : 5.0827 Mean : 5.2261 Mean : 5.2530 Mean : 5.0292 Mean : 4.9990 Mean : 5.0386 Mean : 5.0201
# 3rd Qu.: 7.2458 3rd Qu.: 7.1482 3rd Qu.: 7.2749 3rd Qu.: 7.2045 3rd Qu.: 7.0249 3rd Qu.: 6.8045 3rd Qu.: 7.1026 3rd Qu.: 6.8093
# Max. :16.0300 Max. :16.0264 Max. :15.8995 Max. :15.9624 Max. :15.9858 Max. :15.9348 Max. :15.6545 Max. :15.7622
Try(SlideNamesVec <- get("SlideNamesVec",envir=affylmGUIenvironment))
#for eg: SlideNamesVec is:
#[1] "Abs10.1" "Abs10.2" "Pres10.1" "Pres10.2" "Abs48.1" "Abs48.2" "Pres48.1" "Pres48.2"
#This plotFunction will create a boxplot of Normalized data
Try(
plotFunction <- function(){
Try(opar<-par(bg="white",cex=0.7))
Try(boxplot(data.frame(NormalizedAffyData.exprs),col="blue",las=2,names=SlideNamesVec))
Try(title(plotTitle))
Try(tmp<-par(opar))
}
)
Try(plotTitle<-"Normalized intensity distribution for each slide")
Try(
HTMLplotUsingFunction(
Caption = plotTitle,
File = fileNameWithPath,
GraphRelativeDirectory = HTMLfileRelativePath,
GraphAbsoluteDirectory = HTMLfilePath,
GraphFileName = "NormalizedIntensityBoxPlot",
GraphSaveAs = "png",
GraphBorder = 1,
Align = "left",
plotFunction=plotFunction,
Width=plotWidth,
Height=plotHeight,
PointSize=plotPointSize,
BG=plotBG,
res=plotRes
)
)
#For eg: This writes to HTML file:
# <p align=left><img src='alg_Est_gcrma_3C_files/NormalizedIntensityBoxPlot.png' border=1><br><i> Normalized intensity distribution for each slide </i></P>
#It also creates the file "NormalizedIntensityBoxPlot.png" in the "alg_Est_gcrma_3C_files" subdirectory.
}
if(ExportDesignMatrix){
Try(design <- get("design",envir=affylmGUIenvironment))
#For eg: This gets the design matrix:
# EstAbsent10 EstAbsent48 EstPresent10 EstPresent48
#low10-1.cel 1 0 0 0
#low10-2.cel 1 0 0 0
#high10-1.cel 0 0 1 0
#high10-2.cel 0 0 1 0
#low48-1.cel 0 1 0 0
#low48-2.cel 0 1 0 0
#high48-1.cel 0 0 0 1
#high48-2.cel 0 0 0 1
Try(displayVector <- rep("g",ncol(design)+1)) #This creates: [1] "g" "g" "g" "g" "g"
Try(displayVector[0] <- "s")
Try(DesignXtable <- xtable(design,display=displayVector))
#For eg. This creates:
#% latex table generated in R 2.6.0 by xtable 1.5-1 package
#% Thu Sep 20 22:42:27 2007
#\begin{table}[ht]
#\begin{center}
#\begin{tabular}{rrrrr}
# \hline
# & EstAbsent10 & EstAbsent48 & EstPresent10 & EstPresent48 \\
# \hline
#low10-1.cel & 1 & 0 & 0 & 0 \\
# low10-2.cel & 1 & 0 & 0 & 0 \\
# high10-1.cel & 0 & 0 & 1 & 0 \\
# high10-2.cel & 0 & 0 & 1 & 0 \\
# low48-1.cel & 0 & 1 & 0 & 0 \\
# low48-2.cel & 0 & 1 & 0 & 0 \\
# high48-1.cel & 0 & 0 & 0 & 1 \\
# high48-2.cel & 0 & 0 & 0 & 1 \\
# \hline
#\end{tabular}
#\end{center}
#\end{table}
Try(HTML.title("<a name=\"DesignMatrix\">Design Matrix</a>",HR=2))
# For eg. this writes to HTML file:
# <h2 > <a name="DesignMatrix">Design Matrix</a></h2>
Try(print(DesignXtable,type="html",file=fileNameWithPath,append=TRUE))
#For eg. This writes to HTML file:
#<!-- html table generated in R 2.6.0 by xtable 1.5-1 package -->
#<!-- Thu Sep 20 22:44:52 2007 -->
#<TABLE border=1>
#<TR> <TH> </TH> <TH> EstAbsent10 </TH> <TH> EstAbsent48 </TH> <TH> EstPresent10 </TH> <TH> EstPresent48 </TH> </TR>
# <TR> <TD align="right"> low10-1.cel </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> low10-2.cel </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> high10-1.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> high10-2.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> low48-1.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> low48-2.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> high48-1.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> </TR>
# <TR> <TD align="right"> high48-2.cel </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> </TR>
# </TABLE>
}
if(ExportContrastsMatrix){
Try(displayVector <- rep("g",ncol(contrastsMatrix)+1))
Try(displayVector[0] <- "s")
Try(ContrastsXtable <- xtable(contrastsMatrix,display=displayVector))
Try(HTML.title("<a name=\"ContrastsMatrix\">Contrasts Matrix</a>",HR=2))
Try(print(ContrastsXtable,type="html",file=fileNameWithPath,append=TRUE))
#For eg. In a similar wat to design table, this routine writes this to the HTML file:
# <h2 > <a name="ContrastsMatrix">Contrasts Matrix</a></h2><!-- html table generated in R 2.6.0 by xtable 1.5-1 package -->
#<!-- Thu Sep 20 22:46:48 2007 -->
#<TABLE border=1>
#<TR> <TH> </TH> <TH> (EstAbsent10)-(EstAbsent48) </TH> <TH> (EstPresent10)-(EstPresent48) </TH> <TH> (EstAbsent10)-(EstPresent48) </TH> </TR>
# <TR> <TD align="right"> EstAbsent10 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> </TR>
# <TR> <TD align="right"> EstAbsent48 </TD> <TD align="right"> -1 </TD> <TD align="right"> 0 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> EstPresent10 </TD> <TD align="right"> 0 </TD> <TD align="right"> 1 </TD> <TD align="right"> 0 </TD> </TR>
# <TR> <TD align="right"> EstPresent48 </TD> <TD align="right"> 0 </TD> <TD align="right"> -1 </TD> <TD align="right"> -1 </TD> </TR>
# </TABLE>
}
if(ExportMAPlotsContrasts){
Try(HTML.title("<a name=\"MAPlotsContrasts\">M A Plots for Contrasts</a>",HR=2))
#For eg. This writes to HTML file:
# <h2 > <a name="MAPlotsContrasts">M A Plots for Contrasts</a></h2>
Try(A <- rowMeans(NormalizedAffyData.exprs))
#For eg. This gets rowMeans, as summarized below:
#> summary(A)
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#-0.3351 2.9500 4.1050 5.0970 7.0480 15.9100
Try(pch <- 16) #set character height plot
Try(cex <- 0.2) #set character expansion for plot
Try(
#In this example, create an MA plot for each of the three contrast
for (contrast in (1:NumContrasts)){ #For eg. NumContrasts = 3
Try(plotTitle<-paste("M A Plot (",ContrastNamesVec[contrast],")",sep="")) # ContrastNamesVec = "(EstAbsent10)-(EstAbsent48)" "(EstPresent10)-(EstPresent48)" "(EstAbsent10)-(EstPresent48)"
Try(HTML.title(plotTitle,HR=2))
#For eg. this writes to HTML:
# <h2 > M A Plot ((EstAbsent10)-(EstAbsent48))</h2><p align=left><img src='alg_Est_gcrma_3C_files/contrastMAplot.1.png' border=1><br><i> M A Plot ((EstAbsent10)-(EstAbsent48)) </i></P>
# <h2 > M A Plot ((EstPresent10)-(EstPresent48))</h2><p align=left><img src='alg_Est_gcrma_3C_files/contrastMAplot.2.png' border=1><br><i> M A Plot ((EstPresent10)-(EstPresent48)) </i></P>
# <h2 > M A Plot ((EstAbsent10)-(EstPresent48))</h2><p align=left><img src='alg_Est_gcrma_3C_files/contrastMAplot.3.png' border=1><br><i> M A Plot ((EstAbsent10)-(EstPresent48)) </i></P>
Try(M <- fit$coefficients[,contrast])
#For eg. For contrast no.1, M is:
#> summary(M)
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#-5.303e+00 -9.561e-02 7.819e-05 9.169e-02 2.857e-01 1.168e+01
#> length(M)
#[1] 12625
#Do an MA plot
Try(
plotFunction <- function(){
Try(opar<-par(bg="white"))
Try(plot(A,M,pch=pch,cex=cex,xlab="A",ylab="M",main=plotTitle))
Try(tmp<-par(opar))
}
)
Try(
HTMLplotUsingFunction(
Caption = plotTitle,
File = fileNameWithPath,
GraphRelativeDirectory = HTMLfileRelativePath,
GraphAbsoluteDirectory = HTMLfilePath,
GraphFileName = paste("contrastMAplot.",contrast,sep=""),
GraphSaveAs = "png",
GraphBorder = 1,
Align = "left",
plotFunction=plotFunction,
Width=plotWidth,
Height=plotHeight,
PointSize=plotPointSize,
BG=plotBG,
res=plotRes
)
)
}
)
}
if(ExportTopNNToptables || ExportCompleteToptables){
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
Try(cdfName <- strsplit(cleancdfname(cdfName(RawAffyData)),"cdf")[[1]])
if(!(.cdfName2AnnPkg(cdfName) %in% .packages(all.available=TRUE))){
Try(install.packages(pkgs=.cdfName2AnnPkg(cdfName), lib=.libPaths(), repos=repositories(), dependencies=c("Depends", "Imports")))
Try(assign("cdfName",cdfName,affylmGUIenvironment))
}
Try(cdfenv <- getCdfInfo(RawAffyData))
Try(genelist <- data.frame(ID=I(ls(cdfenv))))
Try(geneNames <- get("geneNames", envir=affylmGUIenvironment))
Try(geneSymbols <- get("geneSymbols",envir=affylmGUIenvironment))
Try(
if(!length(geneNames) || !length(geneSymbols)){
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="watch"))
Try(RawAffyData <- get("RawAffyData",envir=affylmGUIenvironment))
Try(cdfName <- strsplit(cleancdfname(cdfName(RawAffyData)),"cdf")[[1]])
if(!(cdfName %in% .packages(all.available=TRUE))){
Try(install.packages(pkgs=.cdfName2AnnPkg(cdfName), lib=.libPaths(), repos=repositories(), dependencies=c("Depends", "Imports")))###inserted by keith
}
Try(
if( (.cdfName2AnnPkg(cdfName) %in% .packages(all.available=TRUE)) ){
AnnPkg <- .cdfName2AnnPkg(cdfName)
suppressPackageStartupMessages(requireNamespace(AnnPkg,quietly=TRUE))
Try(probeset2GENENAME <- getFromNamespace(paste0(cdfName,"GENENAME"),AnnPkg))
Try(geneNames <- AnnotationDbi::mget(ls(cdfenv),envir=probeset2GENENAME))
Try(geneNames <- unlist(lapply(geneNames,function(x) paste(x,collapse="; "))))
Try(assign("geneNames",geneNames,affylmGUIenvironment))
Try(probeset2SYMBOL <- getFromNamespace(paste0(cdfName,"SYMBOL"),AnnPkg))
Try(geneSymbols <- AnnotationDbi::mget(ls(cdfenv),envir=probeset2SYMBOL))
Try(geneSymbols <- unlist(lapply(geneSymbols,function(x) paste(x,collapse="; "))))
Try(assign("geneSymbols",geneSymbols,affylmGUIenvironment))
Try(genelist <- data.frame(ID=ls(cdfenv),Symbol=geneSymbols,Name=geneNames,stringsAsFactors=FALSE))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}else{
Try(genelist <- data.frame(ID=ls(cdfenv),stringsAsFactors=FALSE))
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
}
)
}else{
Try(genelist <- data.frame(ID=ls(cdfenv),Symbol=geneSymbols,Name=geneNames,stringsAsFactors=FALSE))
}
)
}
if(ExportTopNNToptables){
Try(
HTML.title(
paste("<a name=\"TopNNToptables\">Top ",numberOfGenes," Differentially Expressed Genes for each Contrast in Contrasts Parameterization ",
ContrastParameterizationNamesVec[contrastParameterizationIndex],"</a>",sep=""),
HR=2
)
)
Try(NormalizedAffyData.exprs <- get("NormalizedAffyData.exprs",envir=affylmGUIenvironment))
Try(if(is.null(fit$Amean)) fit$Amean <- rowMeans(NormalizedAffyData.exprs))
Try(fit$genes <- genelist)
for(coef in (1:NumContrasts)){
Try(options(digits=3))
Try(table1 <- topTable(coef=coef,number=numberOfGenes,genelist=genelist,adjust.method=adjustMethod,sort.by=sortBy,fit=fit))
Try(toptableDisplay <- rep("s",ncol(table1)+1))
Try(toptableDisplay[1] <- "d")
Try(
for (i in (2:(ncol(table1)+1))){
Try(if (colnames(table1)[i-1]=="M") toptableDisplay[i] <- "f")
Try(if (colnames(table1)[i-1]=="A") toptableDisplay[i] <- "f")
Try(if (colnames(table1)[i-1]=="t") toptableDisplay[i] <- "f")
Try(if (colnames(table1)[i-1]=="P.Value") toptableDisplay[i] <- "e")
Try(if (colnames(table1)[i-1]=="B") toptableDisplay[i] <- "f")
}
)
Try(toptableXtable <- xtable(table1,display=toptableDisplay))
Try(
HTML.title(
paste(
"Top ",
numberOfGenes,
" Differentially Expressed Genes for ",
ContrastNamesVec[coef],
" sorted by ",
sortBy,
", adjust method = ",
adjustMethod,
".",
sep=""
),
HR=3
)
)
Try(print(toptableXtable,type="html",file=fileNameWithPath,append=TRUE))
}
}
if(ExportCompleteToptables){
Try(
HTML.title(
paste("<a name=\"CompleteToptables\">Complete Tables of Genes Ranked in order of Evidence for Differential Expression for each contrast in Contrasts Parameterization ",ContrastParameterizationNamesVec[contrastParameterizationIndex],"</a>",sep=""),
HR=2
)
)
Try(NormalizedAffyData.exprs <- get("NormalizedAffyData.exprs",envir=affylmGUIenvironment))
Try(
if(!("Amean" %in% names(fit))){
fit$Amean <- rowMeans(NormalizedAffyData.exprs)
}
)
Try(fit$genes <- genelist)
for(coef in (1:NumContrasts)){
Try(options(digits=3))
Try(table1 <- topTable(coef=coef,number=nrow(genelist),genelist=genelist,adjust.method=adjustMethod,sort.by=sortBy,fit=fit))
Try(ToptableAbsoluteFilename <- paste(HTMLfilePath ,.Platform$file.sep,"CompleteToptable_Contrast",coef,".xls",sep=""))
Try(ToptableRelativeFilename <- paste(HTMLfileRelativePath ,.Platform$file.sep,"CompleteToptable_Contrast",coef,".xls",sep=""))
Try(write.table(table1,file=ToptableAbsoluteFilename,quote=FALSE,col.names=NA,sep="\t"))
Try(HTML.title(paste("Complete Table of Genes Ranked in order of Evidence for Differential Expression for ",ContrastNamesVec[coef]),HR=3))
Try(HTMLli(txt=paste("<a href=\"",ToptableRelativeFilename,"\"><b>",paste("CompleteToptable_Contrast",coef,".xls",sep=""),"</b></a>",sep="")))
}
}
Try(tkconfigure(.affylmGUIglobals$ttMain,cursor="arrow"))
Try(tkfocus(.affylmGUIglobals$ttMain))
Try(HTMLhr())
Try(HTMLli(txt="This report was generated by "))
Try(HTMLli(txt=paste("affylmGUI Version",getPackageVersion("affylmGUI"),"(by James Wettenhall), using")))
Try(HTMLli(txt=paste("affy Version",getPackageVersion("affy"),"(by Rafael A. Irizarry, Laurent Gautier and Benjamin Bolstad),")))
Try(HTMLli(txt=paste("affyPLM Version",getPackageVersion("affyPLM"),"(by Benjamin Bolstad),")))
Try(HTMLli(txt=paste("limma Version",getPackageVersion("limma"),"(by Gordon Smyth),")))
Try(HTMLli(txt=paste("R2HTML Version",getPackageVersion("R2HTML"),"(by Eric Lecoutre) and ")))
Try(HTMLli(txt=paste("xtable Version",getPackageVersion("xtable"),"(by David Dahl)")))
Try(HTMLEndFile())
invisible()
}
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