~ubuntu-branches/ubuntu/utopic/r-bioc-cummerbund/utopic

.plotmatrix <- function (data, hexbin=FALSE, mapping = aes())

#Modified from original ggplot2 plotmatrix

{

        grid <- expand.grid(x = 1:ncol(data), y = 1:ncol(data))

        grid <- subset(grid, x != y)

        all <- do.call("rbind", lapply(1:nrow(grid), function(i) {

                                                xcol <- grid[i, "x"]

                                                ycol <- grid[i, "y"]

                                                data.frame(xvar = names(data)[ycol], yvar = names(data)[xcol], 

                                                                x = data[, xcol], y = data[, ycol], data)

                                        }))

        all$xvar <- factor(all$xvar, levels = names(data))

        all$yvar <- factor(all$yvar, levels = names(data))

        densities <- do.call("rbind", lapply(1:ncol(data), function(i) {

                                                data.frame(xvar = names(data)[i], yvar = names(data)[i], 

                                                                x = data[, i])

                                        }))

        mapping <- plyr::defaults(mapping, aes_string(x = "x", y = "y"))

        class(mapping) <- "uneval"

        p <-ggplot(all) + facet_grid(xvar ~ yvar)#, scales = "free")

        

        if(hexbin){ 

                p<- p + geom_hex(mapping,size=1.5,na.rm = TRUE) 

        }else{

                p<- p + geom_point(mapping,alpha=0.2,size=0.8,na.rm=TRUE)

        }

        

        p<- p + stat_density(aes(x = x, 

                                        y = ..scaled.. * diff(range(x)) + min(x)), data = densities, 

                        position = "identity", colour = "grey20", geom = "line")

        

        p

}

 

#.volcanoMatrix <- function(data){

#       part1<-data[,c('gene_id','sample_1','sample_2','value_1','value_2','test_stat','p_value','q_value')]

#       part2<-data.frame(gene_id=part1$gene_id,sample_1=part1$sample_2,sample_2=part1$sample_1,value_1=part1$value_2,value_2=part1$value_1,test_stat=-part1$test_stat,p_value=part1$p_value,q_value=part1$q_value)

#       data<-rbind(part1,part2)

#       myLevels<-union(data$sample_1,data$sample_2)

#       data$sample_1<-factor(data$sample_1,levels=myLevels)

#       data$sample_2<-factor(data$sample_2,levels=myLevels)

#       data$log2_fold_change<-log2(data$value_2/data$value_1)

#       filler<-data.frame(sample_1=factor(myLevels,levels=myLevels),sample_2=factor(myLevels,levels=myLevels),label=as.character(myLevels))

#       filler$label<-as.character(filler$label)

#       mapping <- defaults(mapping, aes_string(x = "log2_fold_change", y = "-log10(p_value)"))

#       class(mapping) <- "uneval"

#       

#       p <-ggplot(data) + geom_point(mapping,na.rm=TRUE,size=0.8) + geom_text(aes(x=0,y=15,label=label),data=filler) + facet_grid(sample_1~sample_2)

#       

#       p

#       

#}