Theme

Heatmap

Heatmaps can be zoomed with the mouse wheel or by dragging. Once zoomed you can drag the Heatmap to a different location with the mouse. You can also drag the dendrograms as well as the overlays to any position in the graph. Samples and variables can also be dragged as long as there are no dendrograms preventing their move. Dendrogram branches can be flipped by clicking at the vertice of the corresponding branch. Press 'ESC' to reset the Heatmap. Boxes around the cells can be hid or have a different width and/or color or can be higlighted. Samples and variable in the heatmaps can be also be separated. The default color spectrum is 'blue-white-red'.

Graph Configuration

{
   "colorSpectrum" : [
      "blue",
      "white",
      "red"
   ],
   "graphType" : "Heatmap",
   "title" : "Simple Heatmap"
}
                

 
 

Graph Configuration

{
   "heatmapCellBoxColor" : "rgb(255,255,255)",
   "title" : "Clustered data",
   "samplesClustered" : true,
   "showTransition" : false,
   "graphType" : "Heatmap",
   "colorSpectrum" : [
      "blue",
      "white",
      "red"
   ],
   "variablesClustered" : true
}
                

 
 

Graph Configuration

{
   "variablesClustered" : true,
   "showVarDendrogram" : false,
   "graphType" : "Heatmap",
   "title" : "Custom color breaks",
   "samplesClustered" : true,
   "heatmapCellBoxColor" : "rgb(255,255,255)",
   "showSmpDendrogram" : false,
   "colorSpectrum" : [
      "blue",
      "white",
      "red"
   ],
   "colorSpectrumBreaks" : [
      1,
      2,
      10
   ]
}
                

 
 

Graph Configuration

{
   "showSmpDendrogram" : false,
   "colorSpectrum" : [
      "magenta",
      "blue",
      "black",
      "red",
      "gold"
   ],
   "title" : "Cluster Heatmap Without Trees",
   "samplesClustered" : true,
   "heatmapCellBox" : false,
   "variablesClustered" : true,
   "graphType" : "Heatmap",
   "showVarDendrogram" : false
}
                

 
 

Graph Configuration

{
   "samplesClustered" : true,
   "title" : "Symetrical Colors in Heatmap",
   "variablesClustered" : true,
   "graphType" : "Heatmap",
   "showVarDendrogram" : false,
   "colorSpectrumZeroValue" : 0,
   "showSmpDendrogram" : false,
   "colorSpectrum" : [
      "magenta",
      "blue",
      "black",
      "red",
      "gold"
   ]
}
                

 
 

Graph Configuration

{
   "heatmapIndicatorPosition" : "topLeft",
   "variablesClustered" : true,
   "graphType" : "Heatmap",
   "colorSmpDendrogramBy" : "Treatment",
   "heatmapIndicatorHeight" : 50,
   "heatmapIndicatorWidth" : 60,
   "samplesClustered" : true,
   "title" : "R Heatmap",
   "colorSpectrum" : [
      "magenta",
      "blue",
      "black",
      "red",
      "gold"
   ],
   "heatmapIndicatorHistogram" : true,
   "colorSpectrumZeroValue" : 0
}
                

 
 

Graph Configuration

{
   "heatmapIndicatorWidth" : 60,
   "heatmapIndicatorHeight" : 50,
   "graphType" : "Heatmap",
   "colorSmpDendrogramBy" : "Treatment",
   "heatmapIndicatorPosition" : "topLeft",
   "variablesClustered" : true,
   "samplesClustered" : true,
   "title" : "Overlays in Heatmap",
   "heatmapIndicatorHistogram" : true,
   "smpOverlays" : [
      "Treatment",
      "Site"
   ],
   "colorSpectrum" : [
      "magenta",
      "blue",
      "black",
      "red",
      "gold"
   ],
   "heatmapSmpSeparateBy" : "Treatment",
   "colorSpectrumZeroValue" : 0
}
                

 
 

Graph Configuration

{
   "showTransition" : false,
   "graphType" : "Heatmap",
   "variablesClustered" : true,
   "heatmapIndicatorPosition" : "topLeft",
   "heatmapIndicatorWidth" : 60,
   "heatmapIndicatorHeight" : 50,
   "highlightVar" : [
      "Probe18",
      "Probe19",
      "Probe20"
   ],
   "samplesClustered" : true,
   "title" : "Highlight cells in Heatmap",
   "smpOverlays" : [
      "Treatment",
      "Site"
   ],
   "colorSpectrum" : [
      "magenta",
      "blue",
      "black",
      "red",
      "gold"
   ],
   "highlightSmp" : [
      "Sample1",
      "Sample2",
      "Sample3",
      "Sample4",
      "Sample5"
   ],
   "heatmapIndicatorHistogram" : true,
   "colorSpectrumZeroValue" : 0,
   "heatmapSmpSeparateBy" : "Treatment"
}
                

 
 

Graph Configuration

{
   "colorSpectrumZeroValue" : 0,
   "smpOverlayProperties" : {
      "Treatment" : {
         "position" : "right"
      },
      "Site" : {
         "position" : "left"
      },
      "Dose" : {
         "type" : "Dotplot",
         "position" : "right",
         "thickness" : 50
      }
   },
   "varOverlays" : [
      "Type",
      "Sens"
   ],
   "colorKey" : {
      "Type" : "YlGn",
      "Site" : "Pastel1",
      "Treatment" : "Accent",
      "Sens" : [
         "white",
         "green"
      ]
   },
   "samplesClustered" : true,
   "title" : "Advanced Overlays in Heatmaps",
   "showTransition" : false,
   "heatmapIndicatorPosition" : "topLeft",
   "variablesClustered" : true,
   "heatmapIndicatorWidth" : 60,
   "heatmapIndicatorHeight" : 50,
   "smpOverlays" : [
      "Treatment",
      "Site",
      "Dose"
   ],
   "colorSpectrum" : [
      "magenta",
      "blue",
      "black",
      "red",
      "gold"
   ],
   "heatmapIndicatorHistogram" : true,
   "graphType" : "Heatmap",
   "varOverlayProperties" : {
      "Type" : {
         "position" : "top"
      },
      "Sens" : {
         "color" : "red",
         "thickness" : 20,
         "position" : "bottom",
         "type" : "Bar"
      }
   }
}
                

 
 

Graph Configuration

{
   "shapeBy" : "Shape",
   "outlineBy" : "Outline",
   "sizeBy" : "Size",
   "sizeByData" : "data4",
   "graphType" : "Heatmap",
   "guides" : true,
   "outlineByData" : "data2",
   "shapeByData" : "data3"
}
                

 
 

Graph Configuration

{
   "showHeatmapIndicator" : false,
   "graphType" : "Heatmap",
   "showLegend" : false,
   "sizeBy" : "Size",
   "sizeByData" : "data",
   "title" : "A good old Northern Blot",
   "colorSpectrum" : [
      "#f0f0f0",
      "#bdbdbd",
      "#636363",
      "#000000"
   ],
   "sizeByContinuous" : true
}
                

 
 

Graph Configuration

{
   "smpOverlayProperties" : {
      "Early" : {
         "type" : "Line",
         "color" : "blue",
         "thickness" : 50,
         "position" : "right"
      },
      "PhaseC" : {
         "position" : "left",
         "thickness" : 50,
         "type" : "Bar"
      },
      "Temp" : {
         "position" : "right",
         "thickness" : 100,
         "type" : "Heatmap",
         "spectrum" : [
            "blue",
            "white",
            "red"
         ]
      },
      "PhaseA" : {
         "position" : "left",
         "thickness" : 50,
         "type" : "Bar"
      },
      "Binary" : {
         "type" : "Default",
         "position" : "left",
         "scheme" : "BlackAndWhite"
      },
      "Continuous" : {
         "position" : "left",
         "spectrum" : [
            "green",
            "white"
         ],
         "type" : "Heatmap"
      },
      "OnTime" : {
         "position" : "right",
         "thickness" : 50,
         "color" : "green",
         "type" : "Line"
      },
      "Late" : {
         "position" : "right",
         "color" : "red",
         "thickness" : 50,
         "type" : "Line"
      },
      "Discrete" : {
         "type" : "Default",
         "thickness" : 30,
         "position" : "left"
      },
      "PhaseB" : {
         "position" : "left",
         "thickness" : 50,
         "type" : "Bar"
      },
      "Boolean" : {
         "position" : "left"
      }
   },
   "smpOverlays" : [
      "PhaseA",
      "PhaseB",
      "PhaseC",
      "-",
      "-",
      "Binary",
      "Boolean",
      "Continuous",
      "Discrete",
      "-",
      "-",
      "Temp",
      "-",
      "-",
      "Early",
      "OnTime",
      "Late"
   ],
   "varOverlays" : [
      "Drug",
      "-",
      "Male",
      "Female",
      "-",
      "Site",
      "-",
      "Conc",
      "-",
      "Desc",
      "-",
      "Even",
      "Odd",
      "-",
      "-",
      "Nice",
      "Ugly",
      "-",
      "-",
      "Cold",
      "Hot"
   ],
   "varLabelScaleFontFactor" : 1.7,
   "varLabelRotate" : 45,
   "graphType" : "Heatmap",
   "showTransition" : false,
   "smpLabelScaleFontFactor" : 1.1,
   "varOverlayProperties" : {
      "Male" : {
         "type" : "Pie",
         "position" : "top",
         "thickness" : 50
      },
      "Hot" : {
         "type" : "StackedPercent",
         "position" : "bottom",
         "color" : "red",
         "thickness" : 50
      },
      "Nice" : {
         "thickness" : 50,
         "color" : "green",
         "position" : "bottom",
         "type" : "Dotplot"
      },
      "Site" : {
         "position" : "top",
         "type" : "Default"
      },
      "Odd" : {
         "thickness" : 50,
         "position" : "bottom",
         "type" : "BarLine"
      },
      "Desc" : {
         "type" : "Text",
         "position" : "bottom"
      },
      "Ugly" : {
         "type" : "Dotplot",
         "thickness" : 50,
         "color" : "black",
         "position" : "bottom"
      },
      "Female" : {
         "thickness" : 50,
         "position" : "top",
         "type" : "Pie"
      },
      "Even" : {
         "position" : "bottom",
         "thickness" : 50,
         "type" : "Bar"
      },
      "Cold" : {
         "type" : "StackedPercent",
         "position" : "bottom",
         "thickness" : 50,
         "color" : "blue"
      },
      "Conc" : {
         "position" : "top",
         "thickness" : 40,
         "type" : "Bar"
      },
      "Drug" : {
         "position" : "top",
         "thickness" : 30,
         "type" : "Increase"
      }
   }
}