################################################################################# SGCP_ezPlot
SGCP_ezPLOT <- function(sgcp, expreData, keep = FALSE,
pdf.file = TRUE, pdfname = "ezSGCP.pdf",
excel.file = TRUE,
xlsxname = "ezSGCP.xlsx", w = 6, h = 6, sr = 2, sc = 2,
ftype = "png", uni = "in",
expressionPCA = TRUE, pointSize1 = .5,
exprePCATitle0 = "Expression Data PCA Without Labels",
exprePCATitle1 = "Expression Data PCA With Initial Labels",
exprePCATitle2 = "Expression Data PCA With Final Labels",
transformedPCA = TRUE, pointSize2 = 0.5,
transformedTitle0 = "Transformed Data PCA Without Labels",
transformedTitle1 = "Transformed Data PCA Initial Labels",
transformedTitle2 = "Transformed Data PCA Final Labels",
conduct = TRUE,
conductanceTitle = "Cluster Conductance Index",
conductx = "clusterLabel", conducty = "conductance index",
clus_num = TRUE,
silhouette_index = FALSE,
silTitle = "Gene Silhouette Index",
silx = "genes", sily = "silhouette index",
jitt1 = TRUE,
jittTitle1 = "Initial GO p-values", jps1 = 3,
jittx1 = "cluster", jitty1 = "-log10 p-value",
jitt2 = TRUE,
jittTitle2 = "Final GO p-values", jps2 = 3,
jittx2 = "module", jitty2 = "-log10 p-value",
density1 = TRUE,
densTitle1 = "Initial GO p-values Density",
densx1 = "cluster", densy1 = "-log10 p-value",
density2 = TRUE,
densTitle2 = "Final GO p-values Density",
densx2 = "module", densy2 = "-log10 p-value",
mean1 = TRUE,
meanTitle1 = "Cluster Performance",
meanx1 = "cluster", meany1 = "mean -log10 p-value",
mean2 = TRUE,
meanTitle2 = "Module Performance",
meanx2 = "module", meany2 = "mean -log10 p-value",
pie1 = TRUE, pieTitle1 = "Initial GO Analysis",
piex1 = "cluster", piey1 = "count", posx1 = 1.8,
pie2 = TRUE, pieTitle2 = "Final GO Analysis",
piex2 = "module", piey2 = "count", posx2 = 1.8
){
pl.final <- list()
wb <- createWorkbook()
pdf.out <- vector(15, mode = "list")
ind <- 1
counter <- 1
############################################# expression PCA plot
if(expressionPCA){
message("plotting PCA of expression data...")
############################################################
expPCA.lab0 <- SGCP_plot_pca(m = expreData, clusLabs = NULL,
tit = exprePCATitle0, ps = pointSize1)
if(excel.file){
wb <- SGCP_plot2excel(expPCA.lab0, wb, "expressionPCAwithNoLabel",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
expPCA.lab0
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(expPCA.lab0) ,
"expressionPCAwithNoLabel"))
}else{ rm(expPCA.lab0) }
############################################################
if(length(sgcp$clustering$dropped.indices)> 0){
expreData <- expreData[-sgcp$clustering$dropped.indices]
}
expPCA.lab1 <- SGCP_plot_pca(m = expreData,
clusLabs = sgcp$clusterLabels$initialClusters,
tit = exprePCATitle1, ps = pointSize1)
if(excel.file){
wb <- SGCP_plot2excel(expPCA.lab1, wb, "expressionPCAwithInitialLabel",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
expPCA.lab1
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(expPCA.lab1) ,
"expressionPCAwithInitialLabel"))
}else{ rm(expPCA.lab1) }
############################################################
if(sgcp$semilabel){
expPCA.lab2<- SGCP_plot_pca(m = expreData,
clusLabs = sgcp$clusterLabels$finalClusters,
tit = exprePCATitle2, ps = pointSize1)
if(excel.file){
wb <- SGCP_plot2excel(expPCA.lab2, wb, "expressionPCAwithFinalLabel",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
expPCA.lab2
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(expPCA.lab2) ,
"expressionPCAwithFinalLabel")) }
}else{ rm(expPCA.lab2)}
} # end of expressionPCA
######################################### transformed PCA plot
if(transformedPCA){
message("plotting PCA of transformed data...")
############################################################
transPCA.lab0 <- SGCP_plot_pca(m = sgcp$clustering$Y,
clusLabs = NULL,
tit = transformedTitle0, ps = pointSize2)
if(excel.file){
wb <- SGCP_plot2excel(transPCA.lab0, wb, "transformedPCAwithNoLabel",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
transPCA.lab0
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(transPCA.lab0) ,
"transformedPCAwithNoLabel"))
}else{ rm(transPCA.lab0)}
############################################################
transPCA.lab1 <- SGCP_plot_pca(m = sgcp$clustering$Y,
clusLabs = sgcp$clusterLabels$initialClusters,
tit = exprePCATitle1, ps = pointSize2)
if(excel.file){
wb <- SGCP_plot2excel(transPCA.lab1, wb, "transformedPCAwithInitialLabel",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
transPCA.lab1
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(transPCA.lab0) ,
"transformedPCAwithInitialLabel"))
}else{ rm(transPCA.lab1) }
############################################################
if(sgcp$semilabel){
transPCA.lab2 <- SGCP_plot_pca(m = sgcp$clustering$Y,
clusLabs = sgcp$clusterLabels$finalClusters,
tit = exprePCATitle2, ps = pointSize2)
if(excel.file){
wb <- SGCP_plot2excel(transPCA.lab2, wb, "transformedPCAwithFinalLabel",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
transPCA.lab2
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(transPCA.lab0) ,
"transformedPCAwithFinalLabel"))
}else{ rm(transPCA.lab2) }
} # end of semilabel
} # end of transformedPCA
################################################ cluster number
if(clus_num){
if(sgcp$clustering$cv == "cvGO" || sgcp$clustering$cv == "cvConductance"){
message("plotting relativeGap, secondOrderGap, additiveGap methods ...")
rg <- sgcp$clustering$clusterNumberPlot$relativeGap
sg <- sgcp$clustering$clusterNumberPlot$secondOrderGap
ag <- sgcp$clustering$clusterNumberPlot$additiveGap
if(excel.file){
wb <- SGCP_plot2excel(ag, wb, "clusterNuumberAdditiveGap",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
ag
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(excel.file){
wb <- SGCP_plot2excel(rg, wb, "clusterNumberRelativeGap",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
rg
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(excel.file){
wb <- SGCP_plot2excel(sg, wb, "clusterNumberSecondOrderGap",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1 }
if(pdf.file){
sg
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(rg) ,"clusterNuumberRelativeGap"),
setNames(list(sg) ,"clusterNumberSecondOrderGap"),
setNames(list(ag) ,"clusterNumberAdditiveGap"))
}else{ rm(rg, sg, ag)}
}else {
message("methods (relativeGap, secondOrderGap, additiveGap) are needed for number of clusters" )
}
}
############################################# cluster Conductance
if(conduct == TRUE){
if(sgcp$clustering$cv == "cvGO" || sgcp$clustering$cv == "cvConductance" ){
message("plotting cluster conductance index...")
conduct_plt <- SGCP_plot_conductance(conduct = sgcp$clustering$conductance,
tit = conductanceTitle,
xname = conductx, yname = conducty)
if(excel.file){
wb <- SGCP_plot2excel(conduct_plt, wb, "clusterConductance",
ind , w, h, ftype, uni, sr, sc)
ind <- ind +1}
if(pdf.file){
conduct_plt
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(conduct_plt) ,
"clusterConductance"))
}else{ rm(conduct_plt)}
}else{ message("cannot plot conductance \n make sure k is NULL in ezSGCP")}
}
######################################### silhouette index
if(silhouette_index){
if(!is.null(sgcp$clustering[["silhouette"]])){
message("plotting cluster silhouette index...")
sil_plt <- SGCP_plot_silhouette(sgcp$clustering$silhouette,
tit = silTitle, xname = silx, yname = sily)
if(excel.file){
wb <- SGCP_plot2excel(sil_plt, wb, "clusterSilhouetteIndex",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
sil_plt
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(sil_plt) ,
"clusterSilhouetteIndex"))
}else{ rm(sil_plt) }
}else {
message("cannot plot silhouette \n, make sure sil is TRUE in ezSGCP")
}
} # end of if silhouette_index
######################################### pvalue jitter1
if(jitt1){
if(sgcp$semilabel == TRUE){
message("plotting initial GO p-values jitters...")
jitt_plt1 <- SGCP_plot_jitter(df = sgcp$initial.GO$GOresults, tit = jittTitle1,
xname = jittx1, yname = jitty1, ps = jps1)
if(excel.file){
wb <- SGCP_plot2excel(jitt_plt1, wb, "InitialGOpvalueJitter",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
jitt_plt1
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(jitt_plt1) ,
"InitialGOpvalueJitter"))
}else{rm(jitt_plt1)}
}else{
message("cannot plot jitter \n, make sure semilabel is TRUE in ezSGCP")
}
}
####################################### pvalue density1
if(density1){
if(sgcp$semilabel == TRUE){
message("plotting initial GO p-values density...")
den_plt1 <- SGCP_plot_density(df = sgcp$initial.GO$GOresults,
tit = densTitle1,
xname = densx1, yname = densy1)
if(excel.file){
wb <- SGCP_plot2excel(den_plt1, wb, "InitialGOpvalueDensity",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
den_plt1
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(den_plt1) ,
"InitialGOpvalueDensity"))
}else{ rm(den_plt1)}
}else{
message("cannot plot density \n, make sure semilabel is TRUE in ezSGC") }
}
######################################## pvalue mean1
if(mean1){
if(sgcp$semilabel == TRUE){
message("plotting cluster performance...")
mean_plt1 <- SGCP_plot_bar(df = sgcp$initial.GO$GOresults, tit = meanTitle1,
xname = meanx1, yname = meany1)
if(excel.file){
wb <- SGCP_plot2excel(mean_plt1, wb, "InitialGOpvalueMean",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
mean_plt1
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(mean_plt1) ,
"InitialGOpvalueMean"))
}else{ rm(mean_plt1)}
}else{
message("cannot plot mean \n, make sure semilabel is TRUE in ezSGCP") }
}
#############################################pvalue pei1
if(pie1){
if(sgcp$semilabel == TRUE){
message("plotting final GO analysis...")
pie_plt1 <- SGCP_plot_pie(df = sgcp$initial.GO$GOresults, tit = pieTitle1,
xname = piex1, yname = piey1, posx = posx1)
if(excel.file){
wb <- SGCP_plot2excel(pie_plt1, wb, "InitialGOAnalysis",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
pie_plt1
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(pie_plt1) ,
"InitialGOAnalysis"))
}else{ rm(pie_plt1)}
}else{
message("cannot plot pie \n, make sure semilabel is TRUE in ezSGCP") }
}
########################################## pvalue jitter2
if(jitt2){
if(sgcp$semilabel == TRUE){
message("plotting final GO p-values jitters...")
jitt_plt2 <- SGCP_plot_jitter(sgcp$final.GO$GOresults, tit = jittTitle2,
xname = jittx2, yname = jitty2, ps = jps2)
if(excel.file){
wb <- SGCP_plot2excel(jitt_plt2, wb, "FinalGOpvalueJitter",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
jitt_plt2
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(jitt_plt2) ,
"FinalGOpvalueJitter"))
}else{rm(jitt_plt2)}
}else{
message("cannot plot jitter \n, make sure semilabel is TRUE in ezSGCP")
}
}
######################################### pvalue density2
if(density2){
if(sgcp$semilabel == TRUE){
message("plotting final GO p-values density...")
den_plt2 <- SGCP_plot_density(df = sgcp$final.GO$GOresults,
tit = densTitle2,
xname = densx2, yname = densy2)
if(excel.file){
wb <- SGCP_plot2excel(den_plt2, wb, "FinalGOpvalueDensity",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
den_plt2
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(den_plt2) ,
"FinalGOpvalueDensity"))
}else{rm(den_plt2)}
}else{
message("cannot plot density \n, make sure semilabel is TRUE in ezSGCP") }
}
##################################### pvalue mean2
if(mean2){
if(sgcp$semilabel == TRUE){
message("plotting module performance...")
mean_plt2 <- SGCP_plot_bar(df = sgcp$final.GO$GOresults, tit = meanTitle2,
xname = meanx2, yname = meany2)
if(excel.file){
wb <- SGCP_plot2excel(mean_plt2, wb, "FinalGOpvalueMean",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
mean_plt2
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(mean_plt2) ,
"FinalGOpvalueMean"))
}else{ rm(mean_plt2)}
}else{
message("cannot plot mean \n, make sure semilabel is TRUE in ezSGCP") }
}
################################################## pvalue pei2
if(pie2){
if(sgcp$semilabel == TRUE){
message("plotting final GO analysis...")
pie_plt2 <- SGCP_plot_pie(df = sgcp$final.GO$GOresults, tit = pieTitle2,
xname = piex2, yname = piey2, posx = posx2)
if(excel.file){
wb <- SGCP_plot2excel(pie_plt2, wb, "FinalGOAnalysis",
ind , w, h, ftype, uni, sr, sc)
ind <- ind + 1}
if(pdf.file){
pie_plt2
pdf.out[[counter]] <- recordPlot()
counter <- counter + 1}
if(keep){
pl.final <- c(pl.final, setNames(list(pie_plt2) ,
"FinalGOAnalysis"))
}else{rm(pie_plt2)}
}else{
message("cannot plot pie \n, make sure semilabel is TRUE in ezSGCP") }
}
###################################
if(excel.file){
SGCP_saveResult(wb, xlsxname)}
if(pdf.file){
pdf(pdfname, onefile = TRUE)
for(plt in pdf.out){
if(!is.null(plt)){
replayPlot(plt)
}
}
graphics.off()
}
if(keep){ return(pl.final) }
} # end of ezPLOT
