Hi all,

This primarily concerns use of the scale bar.

Currently the chosen value on the scale bar colours all the spots with an expression value of greater or equal magnitude with the darkest colour. We believe that this is restrictive as you are not explicitly able to set the value at which colouring starts and also because the colouring mechanism is not transparent (eg. at which values do the different colours apply?).
We believe that expression values with no significance should not be coloured. We also believe that expression values above a certain threshold do not gain much more significance (eg. what does it really matter if a spot is 5x or 1000x upregulated, either way it warrants investigation).
Would it possible to add a feature where you can choose a lower bound, where colouring starts, and a higher bound, where the colours get no darker.

Cheers,
Liam

We have tried to broaden the colour scale as much as possible.

As a result our colours range from diry red to red to white to blue to dirty blue.

You can choose the higher bound of the colour range by using the pathway menu: Pathway -> Options->


A legende for the colour scale is under way so that coulours are transparent.

I guess the trouble we're having is discerning the non-significant spots from the significant spot, especially when the colours get so light you can barely see them.
I realise that you can use the scale bar to make the colours darker, but that also makes all the non-significant spots darker which doesn't solve our problem.

Sorry for the late reply, i've been out of office.

What you want is some kind of having a non linear conversion from colours to values. Currently we have a fixed non linear colour conversion, but we might introduce different colour conversion routines so that we can get conversions which discriminate better for the given data.
The conversion has been optimized for showing log ratios.
Could you tell what values you are visualizing (e.g. log2 )?

We are using log2 values.

Than you should be fine. We have optimized the colour conversion for logarithmic data and tried to broaden the colour range. I don't have an instant solution for that, but we are thinking of methods to increase the dynamic colour range even further.