This page shows a standard expression heatmap, plotted with either d3heatmap
(interactive) [1] or pheatmap
(annotated) [2].
Clustering dendrograms are based on a correlation-based distance matrix using the Spearman coefficient, passed to the 'ward.D2' method of hclust()
function in R [3].
Controls are provided to control the appearance of the heatmap. By default, colors are scaled by row to allow comparison of trends between rows.
Controls are provided to select an experiment and assay, as well as the rows and columns of that matrix. You can also choose to summarise the data, creating means by sample group.
If gene sets have been uploaded, you can also use these controls to create heat maps for pre-defined gene sets from GO, KEGG etc. Just use 'Select genes by' -> 'gene set' and choose from the available options.
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