3.5 years ago by

CRUK, Cambridge, UK

Hello-

The main heatmap plot shows correlation values. DiffBind uses `heatmap.2`

in `ggplots`

for the underlying plot, which by default scales to the range of values. Hence if everything is highly correlated the scale may only include values above 0.9, while in another case there can be anti-correlation and a much different scale between -1 to +1. `heatmap.2 `

doesn't offer a way to specify the scale.

What you can do is re-scale the values using z-scores, either by row or by column. For the correlation heatmaps, the rows and columns are the same (symmetrical square matrix) so it doesn't matter which you choose, but you will always get a scale between -2 and +2. An example:

`> plot(myDBA, scale="row")`

(equivalent to` dba.plotHeatmap(myDBA, scale="row")`

)

Cheers-

Rory