Heatmapper
  • Expression
  • Pairwise
  • Image
  • Geomap
  • Geocoordinate
  • 3D
  • Spatial
  • Spectral
  • About
  • Welcome
  • Heatmap
  • Table
  • Row Dendrogram
  • Column Dendrogram
Help
File Info
Download Table
When enabled, the heatmap visualization is automatically updated on each setting change. It is recommended to disable Auto Update for large, computationally expensive datasets. When disabled, the Auto Update button must be explicitly clicked to update the visualization.
Heatmap
Y-axis Label
Select a column in your data to use for Y-axis labels. Common columns are 'NAME' or 'UNIQID'. Labels can be toggled on/off in the 'Features' section at the bottom of this sidebar.
Clustering Method
Specify the clustering method used to group input data. To enable clustering by row, toggle on 'Row Dendrogram' in the 'Features' section at the bottom of this sidebar. To enable clustering by column, toggle on 'Column Dendrogram'. Disabling the dendrograms displays input data unclustered.

Read more here
Distance Method
Specify a method to calculate the distance between data points.
Read more here
Text Size
Change the text size of all axis labels. Axis labels can be toggled on and off in the 'Features' section at the bottom of this sidebar.
Scale by:
Normalize cell values to either row or column using z-scores. For each row or column, the elements are transformed to have a mean of 0 and a standard deviation of 1. This makes data comparable across rows or columns, which is useful for clustering. Select 'None' to display data without normalization.
Intrpl Method
Specify an interpolation algorithm to apply to the figure. This can cause values to bleed together and appear smoother.
Read more here.
3D
View Elevation
Control whether the plot is 2D or 3D. Any value other than 90 will display the plot in 3D, with the value specifying the elevation angle of the viewer in respect to the model. Change the angle back to 90 to display the plot in 2D.
View Rotation
Change the angle of rotation of the viewer in respect to the model. For 3D plots only.
Zoom
Crop the view. For 3D plots only.
Intrpl Level
Specify a multiplier for the resolution of the 3D plot. For example, a value of 2 will interpolate the data from an NxM to a 2Nx2M, effectively quadrupling the resolution of each data point by interpolating it into 4. This results in a smoother looking plot, but can be computationally expensive for large datasets.
Scaling
Scale the height of all points by the minimum value. This removes negative values and prevents data from extending below the XY plane. For 3D plots only.
Opacity
Change the opacity of the height bars in 3D plots.
Colors
Select colors to use in the heatmap, with the first color representing low values, and the last color representing high values. If the 'Custom' checkbox is enabled you may specify up to 12 colors. A minimum of two colors are needed.
# of Color Bins
Specify the number of color bins to use. A higher number of color bins results in a smoother gradient between neighbouring values. Fewer bins results in more distinct colors.
Features
Row Dendrogram enables clustering of rows. Column Dendrogram enables clustering of columns. X and Y labels toggle the data labels along their respective axes. Z labels toggles the data labels along the Z axis if rendering as a 3D plot. Legend displays a colorbar legend on the heatmap.
Image Settings
Resolution (DPI)
Specify the resolution of the image in pixels per inch. Higher DPI values result in higher quality images, but larger file sizes. This setting affects the heatmap on screen as well as the downloaded plot.
Image Size
Select Custom Width to specify a custom width (in pixels) for the heat map on your screen.

Select Fit to Screen to have the entire heat map visible in your browser window.

Select Expand to expand the heat map so that axis labels for all rows and columns are legible. You may have to scroll to see the entire heat map. 'Expand' can be computationally expensive for large datasets, and overrides the 'Text Size' setting.
Download Heatmap
Orientation