Commits

Anonymous committed d9a2110

deleted accidentally uploaded files

Comments (0)

Files changed (16)

 	move_uploaded_file($_FILES["file7"]["tmp_name"], $file7);
 }
 $c = 0;
-$images = array();
-foreach (glob($outDir . 'hist/*') as $allfile1) {
-	$images[$c] = $allfile1;
-	$c++;
-}
+$images =  glob($outDir . 'hist/*'); 
+usort($images, function($a, $b) {
+	return filemtime($b) < filemtime($a);
+});
 $c = 0;
 $geneFiles = array();
 $linkFiles = array();
 		$linkScript .= "<option value='$file' selected='selected'>$filename</option>";
 	}
 }
-$script ="<script>var colorArray = new Array('rgba(20,83,154, .8)', 'rgba(154,110,9, .8)', 'rgba(29,110,17, .8)', 'rgba(100,20,162, .8)', 'rgba(0,0,0, .8)', 'rgba(100,0,0, .8)', 'rgba(168,168,8, .8)');
+$script ="<script>var colorArray = new Array('rgba(20,83,154, .6)', 'rgba(154,110,9, .6)', 'rgba(29,110,17, .6)', 'rgba(100,20,162, .6)', 'rgba(0,0,0, .6)', 'rgba(100,0,0, .6)', 'rgba(168,168,8, .6)');
 		var c = -1;";
 if (is_file('temp/' . $username . '/relations.txt') == true) {
 	$relations = file_get_contents('temp/' . $username . '/relations.txt');

temp/7:23:19:14:32_R.cmd

-library(RCircos)
-Species <- 'Human';
-if(Species == 'Human') {
-	data(UCSC.HG19.Human.CytoBandIdeogram);
-	cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
-} else if(Species == "Mouse") {
-	data(UCSC.Mouse.GRCm38.CytoBandIdeogram);
-	cyto.info <- UCSC.Mouse.GRCm38.CytoBandIdeogram;
-} else {
-	data(UCSC.Baylor.3.4.Rat.cytoBandIdeogram);
-	cyto.info <- UCSC.Baylor.3.4.Rat.cytoBandIdeogram;
-}
-excChrs <- c();
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- excChrs[excChrs != ""]
-RCircos.Set.Core.Components(cyto.info, chr.exclude=excChrs, 7 + 4, 0);
-rcircos.params <- RCircos.Get.Plot.Parameters();
-rcircos.params$text.size <- 0.4;
-rcircos.params$track.height <- 0.1;
-RCircos.Reset.Plot.Parameters(rcircos.params);
-TrackTypes <- c("Heatmap", "Histogram", "Line", "Scatter", "Tile");
-TrackFiles <- c("temp/dp96r7olatynxxom1swuoex56n/testHeatmap.csv", "temp/dp96r7olatynxxom1swuoex56n/testHistogram.csv", "temp/dp96r7olatynxxom1swuoex56n/testScatter.csv", "temp/dp96r7olatynxxom1swuoex56n/testScatter.csv", "temp/dp96r7olatynxxom1swuoex56n/testTile.csv");
-FileTypes <- c("csv", "csv", "csv", "csv", "csv");
-out.file <- "temp/dp96r7olatynxxom1swuoex56n/hist/7:23:19:14:32.png";
-if('png' == 'pdf') {
-	pdf(file = out.file, width=6, height=6, compress=TRUE);
-} else {
-	png(filename = out.file, width=6, height=6, units="in", res=300, 	type="cairo");
-}
-RCircos.Set.Plot.Area();
-RCircos.Chromosome.Ideogram.Plot();
-linkNumber <- 0;
-c <- 0;
-probe <- F;
-if('on' != '') {
-	if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' =='') {
-		c <- c-3
-		probe <- T;
-		linkNumber <- c;
-	}
-	for( i in 1:5) {
-		TrackType <- TrackTypes[i];
-		TrackFile <- TrackFiles[i];
-		FileType <- FileTypes[i];
-		if(TrackType == "Heatmap" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Heatmap.Plot(TrackData, 6, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Histogram" & TrackFile!='') {
-		c <- c+1;
-		
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Histogram.Plot(TrackData, 4, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Line" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Line.Plot(TrackData, 5, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Scatter" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Scatter.Plot(TrackData, 5, c+3, "in", 1);
-			linkNumber <- c;
-		} else if(TrackType == "Tile" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Tile.Plot(TrackData, c+3, "in");
-			linkNumber <- c;
-		} 
-	}
-} else {
-	for( i in 1:5) {
-		TrackType <- TrackTypes[i];
-		TrackFile <- TrackFiles[i];
-		if(TrackType == "Heatmap" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Heatmap.Plot(TrackData, 6, i + 3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Histogram" & TrackFile!='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Histogram.Plot(TrackData, 4, i+3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Line" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Line.Plot(TrackData, 5, i+3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Scatter" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Scatter.Plot(TrackData, 5, i+3, "in", 1);
-			linkNumber <- i;
-		} else if(TrackType == "Tile" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Tile.Plot(TrackData, i+3, "in");
-			linkNumber <- i;
-		} 
-	}
-}
-if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' == '' & linkNumber == 0 & 'temp/dp96r7olatynxxom1swuoex56n/testLink.csv' != '' & probe == F) {
-	if("csv" == "table") {
-		link.data <- read.table("temp/dp96r7olatynxxom1swuoex56n/testLink.csv", sep="	", quote="", head=T);
-	} else {
-		link.data <- read.csv("temp/dp96r7olatynxxom1swuoex56n/testLink.csv", sep=",", quote="", head=T);
-	}
-	RCircos.Link.Plot(link.data, 1, TRUE);
-} else if('temp/dp96r7olatynxxom1swuoex56n/testLink.csv' != '') {
-	if("csv" == "table") {
-		link.data <- read.table("temp/dp96r7olatynxxom1swuoex56n/testLink.csv", sep="	", quote="", head=T);
-	} else {
-		link.data <- read.csv("temp/dp96r7olatynxxom1swuoex56n/testLink.csv", sep=",", quote="", head=T);
-	}
-		RCircos.Link.Plot(link.data, 4 + linkNumber, TRUE);	
-}
-if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' !='') {
-	if("csv" == "table") {
-		gene.data <- read.table("temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv", sep="	", quote="", head=T);
-	} else {
-		gene.data <- read.csv("temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv", sep=",", quote="", head=T);
-	}
-	RCircos.Gene.Connector.Plot(gene.data, 1, "in");
-	RCircos.Gene.Name.Plot(gene.data, 4, 2,"in");
-}
-
-dev.off();

temp/7:23:19:38:5_R.cmd

-library(RCircos)
-Species <- 'Human';
-if(Species == 'Human') {
-	data(UCSC.HG19.Human.CytoBandIdeogram);
-	cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
-} else if(Species == "Mouse") {
-	data(UCSC.Mouse.GRCm38.CytoBandIdeogram);
-	cyto.info <- UCSC.Mouse.GRCm38.CytoBandIdeogram;
-} else {
-	data(UCSC.Baylor.3.4.Rat.cytoBandIdeogram);
-	cyto.info <- UCSC.Baylor.3.4.Rat.cytoBandIdeogram;
-}
-excChrs <- c();
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- excChrs[excChrs != ""]
-RCircos.Set.Core.Components(cyto.info, chr.exclude=excChrs, 4 + 4, 0);
-rcircos.params <- RCircos.Get.Plot.Parameters();
-rcircos.params$text.size <- 0.4;
-rcircos.params$track.height <- 0.1;
-RCircos.Reset.Plot.Parameters(rcircos.params);
-TrackTypes <- c("Heatmap", "Histogram", "Line", "Scatter", "Tile");
-TrackFiles <- c("temp/dp96r7olatynxxom1swuoex56n/testHeatmap.csv", "", "temp/dp96r7olatynxxom1swuoex56n/testLine.csv", "temp/dp96r7olatynxxom1swuoex56n/testLine.csv", "");
-FileTypes <- c("csv", "", "csv", "csv", "");
-out.file <- "temp/dp96r7olatynxxom1swuoex56n/hist/7:23:19:38:5.png";
-if('png' == 'pdf') {
-	pdf(file = out.file, width=6, height=6, compress=TRUE);
-} else {
-	png(filename = out.file, width=6, height=6, units="in", res=300, 	type="cairo");
-}
-RCircos.Set.Plot.Area();
-RCircos.Chromosome.Ideogram.Plot();
-linkNumber <- 0;
-c <- 0;
-probe <- F;
-if('on' != '') {
-	if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' =='') {
-		c <- c-3
-		probe <- T;
-		linkNumber <- c;
-	}
-	for( i in 1:5) {
-		TrackType <- TrackTypes[i];
-		TrackFile <- TrackFiles[i];
-		FileType <- FileTypes[i];
-		if(TrackType == "Heatmap" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Heatmap.Plot(TrackData, 6, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Histogram" & TrackFile!='') {
-		c <- c+1;
-		
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Histogram.Plot(TrackData, 4, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Line" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Line.Plot(TrackData, 5, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Scatter" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Scatter.Plot(TrackData, 5, c+3, "in", 1);
-			linkNumber <- c;
-		} else if(TrackType == "Tile" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Tile.Plot(TrackData, c+3, "in");
-			linkNumber <- c;
-		} 
-	}
-} else {
-	for( i in 1:5) {
-		TrackType <- TrackTypes[i];
-		TrackFile <- TrackFiles[i];
-		if(TrackType == "Heatmap" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Heatmap.Plot(TrackData, 6, i + 3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Histogram" & TrackFile!='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Histogram.Plot(TrackData, 4, i+3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Line" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Line.Plot(TrackData, 5, i+3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Scatter" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Scatter.Plot(TrackData, 5, i+3, "in", 1);
-			linkNumber <- i;
-		} else if(TrackType == "Tile" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Tile.Plot(TrackData, i+3, "in");
-			linkNumber <- i;
-		} 
-	}
-}
-if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' == '' & linkNumber == 0 & '' != '' & probe == F) {
-	if("" == "table") {
-		link.data <- read.table("", sep="	", quote="", head=T);
-	} else {
-		link.data <- read.csv("", sep=",", quote="", head=T);
-	}
-	RCircos.Link.Plot(link.data, 1, TRUE);
-} else if('' != '') {
-	if("" == "table") {
-		link.data <- read.table("", sep="	", quote="", head=T);
-	} else {
-		link.data <- read.csv("", sep=",", quote="", head=T);
-	}
-		RCircos.Link.Plot(link.data, 4 + linkNumber, TRUE);	
-}
-if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' !='') {
-	if("csv" == "table") {
-		gene.data <- read.table("temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv", sep="	", quote="", head=T);
-	} else {
-		gene.data <- read.csv("temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv", sep=",", quote="", head=T);
-	}
-	RCircos.Gene.Connector.Plot(gene.data, 1, "in");
-	RCircos.Gene.Name.Plot(gene.data, 4, 2,"in");
-}
-
-dev.off();

temp/7:23:19:40:9_R.cmd

-library(RCircos)
-Species <- 'Human';
-if(Species == 'Human') {
-	data(UCSC.HG19.Human.CytoBandIdeogram);
-	cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
-} else if(Species == "Mouse") {
-	data(UCSC.Mouse.GRCm38.CytoBandIdeogram);
-	cyto.info <- UCSC.Mouse.GRCm38.CytoBandIdeogram;
-} else {
-	data(UCSC.Baylor.3.4.Rat.cytoBandIdeogram);
-	cyto.info <- UCSC.Baylor.3.4.Rat.cytoBandIdeogram;
-}
-excChrs <- c();
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");excChrs <- append(excChrs, "");
-excChrs <- excChrs[excChrs != ""]
-RCircos.Set.Core.Components(cyto.info, chr.exclude=excChrs, 4 + 4, 0);
-rcircos.params <- RCircos.Get.Plot.Parameters();
-rcircos.params$text.size <- 0.4;
-rcircos.params$track.height <- 0.1;
-RCircos.Reset.Plot.Parameters(rcircos.params);
-TrackTypes <- c("Heatmap", "Histogram", "Line", "Scatter", "Tile");
-TrackFiles <- c("temp/dp96r7olatynxxom1swuoex56n/testHeatmap.csv", "", "temp/dp96r7olatynxxom1swuoex56n/testLine.csv", "temp/dp96r7olatynxxom1swuoex56n/testLine.csv", "");
-FileTypes <- c("csv", "", "csv", "csv", "");
-out.file <- "temp/dp96r7olatynxxom1swuoex56n/hist/7:23:19:40:9.pdf";
-if('pdf' == 'pdf') {
-	pdf(file = out.file, width=6, height=6, compress=TRUE);
-} else {
-	pdf(filename = out.file, width=6, height=6, units="in", res=300, 	type="cairo");
-}
-RCircos.Set.Plot.Area();
-RCircos.Chromosome.Ideogram.Plot();
-linkNumber <- 0;
-c <- 0;
-probe <- F;
-if('on' != '') {
-	if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' =='') {
-		c <- c-3
-		probe <- T;
-		linkNumber <- c;
-	}
-	for( i in 1:5) {
-		TrackType <- TrackTypes[i];
-		TrackFile <- TrackFiles[i];
-		FileType <- FileTypes[i];
-		if(TrackType == "Heatmap" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Heatmap.Plot(TrackData, 6, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Histogram" & TrackFile!='') {
-		c <- c+1;
-		
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Histogram.Plot(TrackData, 4, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Line" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Line.Plot(TrackData, 5, c+3, "in");
-			linkNumber <- c;
-		} else if(TrackType == "Scatter" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Scatter.Plot(TrackData, 5, c+3, "in", 1);
-			linkNumber <- c;
-		} else if(TrackType == "Tile" & TrackFile !='') {
-		c <- c+1;
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Tile.Plot(TrackData, c+3, "in");
-			linkNumber <- c;
-		} 
-	}
-} else {
-	for( i in 1:5) {
-		TrackType <- TrackTypes[i];
-		TrackFile <- TrackFiles[i];
-		if(TrackType == "Heatmap" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Heatmap.Plot(TrackData, 6, i + 3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Histogram" & TrackFile!='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Histogram.Plot(TrackData, 4, i+3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Line" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Line.Plot(TrackData, 5, i+3, "in");
-			linkNumber <- i;
-		} else if(TrackType == "Scatter" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Scatter.Plot(TrackData, 5, i+3, "in", 1);
-			linkNumber <- i;
-		} else if(TrackType == "Tile" & TrackFile !='') {
-			if(FileType == "table") {
-				TrackData <- read.table(TrackFile, sep="	", quote="", head=T);
-			} else {
-				TrackData <- read.csv(TrackFile, sep=",", quote="", head=T);
-			}
-			RCircos.Tile.Plot(TrackData, i+3, "in");
-			linkNumber <- i;
-		} 
-	}
-}
-if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' == '' & linkNumber == 0 & '' != '' & probe == F) {
-	if("" == "table") {
-		link.data <- read.table("", sep="	", quote="", head=T);
-	} else {
-		link.data <- read.csv("", sep=",", quote="", head=T);
-	}
-	RCircos.Link.Plot(link.data, 1, TRUE);
-} else if('' != '') {
-	if("" == "table") {
-		link.data <- read.table("", sep="	", quote="", head=T);
-	} else {
-		link.data <- read.csv("", sep=",", quote="", head=T);
-	}
-		RCircos.Link.Plot(link.data, 4 + linkNumber, TRUE);	
-}
-if('temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv' !='') {
-	if("csv" == "table") {
-		gene.data <- read.table("temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv", sep="	", quote="", head=T);
-	} else {
-		gene.data <- read.csv("temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv", sep=",", quote="", head=T);
-	}
-	RCircos.Gene.Connector.Plot(gene.data, 1, "in");
-	RCircos.Gene.Name.Plot(gene.data, 4, 2,"in");
-}
-
-dev.off();

temp/dp96r7olatynxxom1swuoex56n/hist/7:23:19:14:32.png

Removed
Old image

temp/dp96r7olatynxxom1swuoex56n/hist/7:23:19:38:5.png

Removed
Old image

temp/dp96r7olatynxxom1swuoex56n/hist/7:23:19:40:9.pdf

Binary file removed.

temp/dp96r7olatynxxom1swuoex56n/relations.txt

-var relArray = new Array('7:23:19:14:32' ,'testGeneLabel');~var relArray = new Array('7:23:19:38:5' ,'testLine','testLine','testGeneLabel');~var relArray = new Array('7:23:19:40:9' ,'testLine','testLine','testGeneLabel');~

temp/dp96r7olatynxxom1swuoex56n/testGeneLabel.csv

-Chromosome,chromStart,chromEnd,Gene
-chr1,8921418,8934967,ENO1
-chr1,17345375,17380514,SDHB
-chr1,27022894,27107247,ARID1A
-chr1,41976121,42501596,HIVEP3
-chr1,43803519,43818443,MPL
-chr1,45794977,45805926,MUTYH
-chr1,65300244,65351947,JAK1
-chr1,97544531,98386478,DPYD
-chr1,110230495,110235917,GSTM1
-chr1,115251155,115258781,NRAS
-chr1,120457928,120612020,NOTCH2
-chr1,155158610,155162634,MUC1
-chr1,155917732,155948218,ARHGEF2
-chr1,156615846,156628926,BCAN
-chr1,156639113,156647056,NES
-chr1,156737563,156770252,PRCC
-chr1,161284195,161332330,SDHC
-chr1,185056685,185069433,RNF2
-chr1,186643484,186649422,PTGS2
-chr1,193091330,193219842,CDC73
-chr1,208061082,208084425,CD34
-chr1,241661127,241683022,FH
-chr10,8097618,8115986,GATA3
-chr10,17271421,17279270,VIM
-chr10,35299238,35363154,CUL2
-chr10,43572706,43623717,RET
-chr10,89624226,89725229,PTEN
-chr10,104263909,104389912,SUFU
-chr10,114710515,114925731,TCF7L2
-chr10,121411187,121436794,BAG3
-chr10,123239094,123357972,FGFR2
-chr10,124320286,124402914,DMBT1
-chr10,129897453,129923931,MKI67
-chr10,131265479,131565261,MGMT
-chr11,532635,534322,HRAS
-chr11,1074901,1104263,MUC2
-chr11,10819362,10828842,EIF4G2
-chr11,11986010,12030129,DKK3
-chr11,32410603,32456891,WT1
-chr11,61197618,61213543,SDHAF2
-chr11,64571805,64577581,MEN1
-chr11,69456081,69466050,CCND1
-chr11,100909846,100999801,PGR
-chr11,108098351,108236235,ATM
-chr11,111957631,111965694,SDHD
-chr11,119077127,119170491,CBL
-chr12,7024996,7031963,ENO2
-chr12,25362728,25398318,KRAS
-chr12,46582752,46633583,SLC38A1
-chr12,52345527,52387894,ACVR1B
-chr12,54575302,54582778,SMUG1
-chr12,56474084,56495839,ERBB3
-chr12,58142307,58145500,CDK4
-chr12,112856915,112942568,PTPN11
-chr12,121416571,121438995,HNF1A
-chr13,28537251,28543143,CDX2
-chr13,28578188,28674647,FLT3
-chr13,32890597,32972907,BRCA2
-chr13,48878048,49054207,RB1
-chr13,113777169,113803831,F10
-chr14,81422024,81610697,TSHR
-chr14,105236677,105258980,AKT1
-chr15,59172197,59225764,SLTM
-chr15,63618483,63673919,CA12
-chr15,75012829,75015438,CYP1A1
-chr15,90627497,90645622,IDH2
-chr16,2098616,2138611,TSC2
-chr16,11348699,11349335,SOCS1
-chr16,29841870,29859310,MVP
-chr16,50783609,50830419,CYLD
-chr16,55690606,55739184,SLC6A2
-chr16,66995210,67006952,CES3
-chr16,68771318,68867402,CDH1
-chr17,7462356,7464322,TNFSF13
-chr17,7572926,7579912,TP53
-chr17,11924203,12044577,MAP2K4
-chr17,17116968,17131451,FLCN
-chr17,26646265,26653819,TMEM97
-chr17,29422327,29701173,NF1
-chr17,37856491,37884297,ERBB2
-chr17,38171727,38174066,CSF3
-chr17,39032612,39041437,KRT20
-chr17,41197694,41277340,BRCA1
-chr17,42984714,42992854,GFAP
-chr17,66511540,66526590,PRKAR1A
-chr18,19321544,19444627,MIB1
-chr18,48573416,48604837,SMAD4
-chr18,49867157,51057023,DCC
-chr18,56887497,56897700,GRP
-chr18,60795857,60985899,BCL2
-chr19,1206912,1226646,STK11
-chr19,1438424,1440461,RPS15
-chr19,2717207,2717804,DIRAS1
-chr19,3094649,3121177,GNA11
-chr19,3522987,3534834,FZR1
-chr19,10461509,10489082,TYK2
-chr19,11094827,11172492,SMARCA4
-chr19,16178434,16212156,TPM4
-chr19,17937551,17955226,JAK3
-chr19,33792243,33793320,CEBPA
-chr19,36486176,36486524,SDHAF1
-chr19,42181339,42192094,CEACAM7
-chr19,44047543,44079610,XRCC1
-chr19,52693349,52729678,PPP2R1A
-chr19,58570609,58579829,ZNF135
-chr2,25457147,25536853,DNMT3A
-chr2,29416089,30143525,ALK
-chr2,42396751,42557347,EML4
-chr2,47630330,47710088,MSH2
-chr2,48010372,48033999,MSH6
-chr2,209101802,209116275,IDH1
-chr2,212248339,213403254,ERBB4
-chr2,220283184,220290712,DES
-chr20,4155702,4168054,SMOX
-chr20,5095928,5100444,PCNA
-chr20,30946578,31025141,ASXL1
-chr20,36012556,36031782,SRC
-chr20,57415161,57486247,GNAS
-chr20,62496718,62522898,TPD52L2
-chr21,36164431,36421196,RUNX1
-chr21,39739556,39947624,ERG
-chr22,24129356,24176367,SMARCB1
-chr22,29999987,30090791,NF2
-chr3,10183531,10191649,VHL
-chr3,37035038,37092144,MLH1
-chr3,38180152,38182777,MYD88
-chr3,41265559,41280833,CTNNB1
-chr3,47058582,47205414,SETD2
-chr3,52436303,52443894,BAP1
-chr3,52582078,52713727,PBRM1
-chr3,59737951,60522695,FHIT
-chr3,65342052,66023983,MAGI1
-chr3,122514039,122598225,DIRC2
-chr3,124482469,124605847,ITGB5
-chr3,128199861,128205874,GATA2
-chr3,138664433,138665564,FOXL2
-chr3,150321149,150344921,SELT
-chr3,178916613,178952152,PIK3CA
-chr3,187386852,187388079,SST
-chr4,1795661,1808989,FGFR3
-chr4,41747823,41750627,PHOX2B
-chr4,55124935,55161439,PDGFRA
-chr4,55524181,55604723,KIT
-chr4,55946107,55991460,KDR
-chr4,106155099,106197676,TET2
-chr4,110834491,110932611,EGF
-chr4,123372906,123377595,IL2
-chr4,153244032,153332955,FBXW7
-chr5,218470,256535,SDHA
-chr5,112043414,112179823,APC
-chr5,112214482,112257887,REEP5
-chr5,138117613,138269778,CTNNA1
-chr5,149433631,149465990,CSF1R
-chr5,170814952,170837569,NPM1
-chr6,33286519,33290691,DAXX
-chr6,41652336,41658951,TFEB
-chr6,69348567,70098783,BAI3
-chr6,138192364,138202456,TNFAIP3
-chr7,2946271,2998140,CARD11
-chr7,6013029,6048737,PMS2
-chr7,55086970,55273310,EGFR
-chr7,96747035,96810527,ACN9
-chr7,100663416,100701325,MUC17
-chr7,107531695,107559704,DLD
-chr7,116339138,116436178,MET
-chr7,128388408,128409221,CALU
-chr7,128828992,128852292,SMO
-chr7,140434396,140624503,BRAF
-chr7,148504737,148544390,EZH2
-chr8,18074402,18080429,NAT1
-chr8,18257513,18258386,NAT2
-chr8,22547985,22550457,EGR3
-chr8,23702282,23712036,STC1
-chr8,38271145,38318624,FGFR1
-chr8,125487350,125499885,RNF139
-chr8,128748839,128753204,MYC
-chr9,5021987,5126791,JAK2
-chr9,21440506,21441076,IFNA1
-chr9,21968227,21994330,CDKN2A
-chr9,35673956,35681022,CA9
-chr9,80336238,80646151,GNAQ
-chr9,98209193,98279102,PTCH1
-chr9,133589706,133761070,ABL1
-chr9,135771621,135804259,TSC1
-chr9,139390522,139440238,NOTCH1
-chrX,1314886,1331527,CRLF2
-chrX,48649516,48652571,GATA1
-chrX,48887668,48900752,TFE3
-chrX,49047893,49056645,SYP
-chrX,63409758,63413166,FAM123B
-chrX,76763828,77041487,ATRX
-chrX,153068807,153095753,PDZD4

temp/dp96r7olatynxxom1swuoex56n/testLine.csv

-chromosome,start,stop,num.mark,seg.mean
-1,61735,16895627,8732,0.1797
-1,16896821,17212714,105,-0.2117
-1,17214822,25574471,5321,0.1751
-1,25574707,25662212,37,0.5064
-1,25663310,30741496,2400,0.1384
-1,30741656,30745210,3,-1.4742
-1,30747576,72768916,26451,0.1616
-1,72768936,72811148,45,-1.2602
-1,72811904,81888456,5784,0.1571
-1,81888602,81888605,2,-2.5735
-1,81888667,83885493,1347,0.1567
-1,83886390,83888575,2,-1.2434
-1,83889370,100817103,10923,0.162
-1,100817279,100822030,2,-1.2437
-1,100822776,106013376,2965,0.1507
-1,106019205,106022375,17,0.7119
-1,106024055,110187228,2642,0.1545
-1,110192766,110227515,26,0.4806
-1,110232974,110244998,19,1.2853
-1,110246126,210071062,48711,0.1221
-1,210081613,210082065,2,-1.6726
-1,210083984,240391740,21185,0.0688
-1,240394015,240394139,6,-0.7298
-1,240396105,249224388,5929,0.0644
-10,72759,150544,30,0.6233
-10,152201,13024366,10878,0.1954
-10,13025718,13026114,2,-1.278
-10,13026118,13049245,14,0.1839
-10,13049486,13050610,12,-0.2785
-10,13053686,13107320,77,0.1405
-10,13107408,13496244,287,0.4068
-10,13496479,16467242,2495,0.1132
-10,16470893,16470933,2,-1.4658
-10,16476271,17894976,1080,0.1941
-10,17927554,17949857,3,-1.0162
-10,17971816,18173963,13,-0.0052
-10,18185123,18199813,3,1.0369
-10,18223647,18975700,635,0.0986
-10,18976630,21990586,2267,0.3869
-10,21993991,24375263,1440,0.1117
-10,24377674,24377921,10,1.1332
-10,24378054,29628552,3763,0.0965
-10,29628966,30821673,952,-0.2409
-10,30824955,43302672,5560,0.1304
-10,43306235,44806054,1066,-0.1678
-10,44809197,44810629,6,-1.3362
-10,44811095,73451597,18473,-0.1737
-10,73451659,74023720,349,0.1626
-10,74024526,74025367,2,-1.0273
-10,74027540,82056743,4880,0.164
-10,82057988,82889783,606,-0.2148
-10,82894469,135506704,36155,0.1781
-11,198510,4970367,2474,-0.6051
-11,4972005,4976272,23,-1.7091
-11,4976334,15737746,8105,-0.64
-11,15738775,28472375,9409,0.1608
-11,28477936,32328596,2458,-0.6469
-11,32328926,36441269,3225,0.1552
-11,36441753,37386039,726,0.6654
-11,37394934,37497574,49,-0.5788
-11,37504464,42897932,3569,0.1509
-11,42900322,48354518,3232,-0.182
-11,48355132,48598422,98,0.1502
-11,48601434,48602676,2,-1.798
-11,48606318,51195051,849,0.1818
-11,51205141,55363340,376,-0.1749
-11,55374032,55442318,48,0.1302
-11,55444211,59408942,2409,-0.19
-11,59412424,60198721,534,0.1646
-11,60198990,60965476,470,-0.1748
-11,60984460,61000494,2,1.3032
-11,61015806,70813928,4550,-0.1785
-11,70820759,70892586,41,-0.6806
-11,70892789,70950821,47,0.6545
-11,70956327,71027992,53,-0.683
-11,71028519,71277494,200,0.2054
-11,71277826,71482054,75,-0.6022
-11,71513455,71757247,112,0.155
-11,71758652,72053636,139,-0.6086
-11,72059705,72118294,26,0.5572
-11,72121530,72227849,54,-0.6759
-11,72231558,79967513,4589,0.4114
-11,79967548,79967564,2,-3.2575
-11,79967686,82605135,2085,0.3217
-11,82618283,82619649,5,-0.775
-11,82624090,82679849,31,-0.2016
-11,82680797,83604840,566,-0.6596
-11,83604906,83831259,167,-0.1309
-11,83833466,87017001,2146,-0.6825
-11,87018161,87072098,30,-0.2369
-11,87073016,87858362,555,-0.6709
-11,87859966,87940349,80,-0.2096
-11,87944005,89249899,839,0.1189
-11,89249937,89550224,128,-0.2418
-11,89567541,90116494,186,-0.7301
-11,90117826,93172673,2241,-0.21
-11,93172918,93741295,440,-0.7575
-11,93745306,93819040,40,0.6199
-11,93820905,96658136,1941,-0.7635
-11,96658692,96833343,128,-0.1988
-11,96833589,96870205,34,-0.6935
-11,96870233,96974220,46,-0.237
-11,96974927,96993825,15,-1.0246
-11,96993880,97161982,147,-0.2218
-11,97165756,97542802,282,-0.6663
-11,97556389,97610270,28,0.6055
-11,97613761,97625084,15,-0.6478
-11,97632649,98139807,400,0.7665
-11,98141636,98168748,26,1.4456
-11,98173437,98322952,91,0.8161
-11,98323997,98522768,145,0.4049
-11,98532199,98610481,56,0.776
-11,98611186,98878019,206,0.3815
-11,98878948,99527939,516,0.0659
-11,99530431,99554813,25,0.34
-11,99555393,99596845,34,0.8916
-11,99597565,99605161,11,0.2311
-11,99609646,99654777,25,0.6666
-11,99658272,100298273,485,0.2169
-11,100298421,100339408,24,0.6685
-11,100340318,100910692,474,0.2402
-11,100912322,100932009,56,-0.6886
-11,100932426,100961011,75,0.1435
-11,100961827,101417871,379,-0.7112
-11,101424576,101424670,2,-2.74
-11,101426539,101478097,31,-0.7736
-11,101483577,101824124,250,0.5248
-11,101828156,101873452,34,-0.8923
-11,101876810,102545247,394,0.5636
-11,102551709,102661595,97,-0.7064
-11,102665331,102666316,4,0.1506
-11,102669645,102695486,28,-0.7591
-11,102698557,102885182,128,-0.267
-11,102886098,102916367,18,-0.6538
-11,102917858,102938051,12,0.3078
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