Preview & Heatmap

For a given file, access the Preview function from the File menu or right-click pop-up menu. You can preview any plain text based or binary file and, depending on file data type, a heatmap of the entire dataset in the secondary Heatmap tab (Screenshot). GenomeSpace automatically converts binary text to plain text in the Preview pane.

Previews are up to the first 5 kilobytes.

• Use the horizontal scroll bar to view columns across the file.
• Alternatively, preview in a spread-sheet format, up to the first ten rows of a delimited file, with Extract Rows & Columns.
• SAM files will show the header section and some lines of reads.
• Display of BAM files, although binary formats of SAM, are not currently supported.

Heatmaps are created by jHeatmap and are possible for gct matrix format files or a format that can be converted to GCT, such as GXP and Genomica tab formatted files.

• The colors are row normalized.
• The blue-to-white-to-red heatmap scale matches lower to higher values, respectively.
• GCT file formats provide two columns to describe probes or targets, and the Heatmap preview allows selection of either column to display on the y-axis from a drop-down menu.
• Mouse-scroll within the heatmap to zoom view.
• Click on a datapoint in the heatmap for column, row, and value.

Depending on the dataset size, the heatmap may require some moments to load. Try mouse clicking or scrolling within the heatmap area to display a portion of the heatmap. Files ~5MB should display immediately. Related, depending on your browser memory settings, extremely large files may fail to display. If you see a blank outline, please let us know at gs-help@broadinstitute.org so we can determine the source of error.

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