DiffBind is wonderful that can cluster my H3K27ac ChIP-Seq samples very well as below fig1. However, is there any method or other tool I can use to swap the branches? I would like that my samples could be ordered following the time-series, i.e. 24hr and 48 hr on the right, and 6hr, 12hr, and 18hr on the left. In addition, how can I enlarge the text size, i.e. 0h, 6hr, 12hr, 18hr, 24hr, 48hr, and Condition? May I change the color for each Condition? Many thanks.

fig1

The colors may be changed directly by setting the colSideCols parameter in dba.plotHeatmap().

If you want to re-order the samples, the best way is to use the correlation matrix returned from dba,plotHeatmap(), re-order it as you wish, and plot your own heatmap (using heatmap(), or heatmap.2(), or heatmap.3()) with the Rowv and Colv parameters set to NA.

-Rory