How to set min/max colour gradient for cell plot

Question

Hello,

I have cell plots from a table, in groups.

The cells are coloured by gradient according to the min/max in a group; each group has a different min/max.

Is it possible to set each group to have the same min/max colour gradient?

Thank you in advance

ezorlo · Answer

Dear Jim,

As a matter of fact I did something very similar! I manually changed the extreme values to a max and min of 10 and -10, respectively. That way the legend is the same for all graphs. and I preserve sensitivity to changes that are close to the middle (0) Here is the result:

This is a publication ready graph after much manipulation. I really wish there was more integration between the cell plot which creates nicely standardized color maps and graph builder functionality (e.g. legend labels etc)

thanks again for your help,

txnelson · Answer

You can accomplish the graph colorization the way you want, by creating a transform column. In the example below, the data table has Column 1 with a range of 7.3-93.9, while Column 2 has a range of 28.4-73.9. As can be seen in the Cell plot, the color patterns are very different for ranges of Column 1 and Column 2. However, when Column 2 is transformed, the color ranges are the same. The key is to create the transform column using the following formula If( :Column 1 < 25, x = Col Min( :Column 2 ), :Column 1 > 75, x = Col Max( :Column 2 ), x = :Column 1 ); x; From a scripting standpoint, if you wanted to create a Cell Plot on Column 1 and Column 2, but restrict the color rage to the smaller range from Column 2, here is the script that would do that Cell Plot( Scale Uniformly( 0 ), Center at zero( 0 ), Y( :Column 2, Transform Column( "Transform[Column 2]", Formula( If( :Column 1 < 25, x = Col Min( :Column 2 ), :Column 1 > 75, x = Col Max( :Column 2 ), x = :Column 1 ); x; ) ) ), Legend( 1 ) );

ezorlo · Answer

Dear Jim,

This kind of plot would do the trick of multiple Y axes

However the scaling problem mentioned by charleslean is not easily overcome!

Is there a script I can use, because 1) uniform scaling does not work since it makes the range too wide and 2) I did not understand how to implement cell color according to nominal modeling.

Here is the cell plot script output from the dialog menu:

Cell Plot(
Scale Uniformly( 1 ), // Ideally there should be a way to set max and min range for the color plot here
Center at zero( 1 ),
Y( :Name( "% of transcript" ) ),
X( :Function Class ),
Label( :Gene Ontology, :Function ),
Legend( 1 ),
SendToReport(
Dispatch( {}, "Cell Plot Report", FrameBox, {Frame Size( 616, 106 )} ),
Dispatch( {}, "Cell Plot Report", FrameBox( 3 ), {Frame Size( 616, 106 )} ),
Dispatch( {}, "Cell Plot Report", FrameBox( 5 ), {Frame Size( 616, 106 )} ),
Dispatch( {}, "", NumberColBox, {Set Format( "Fixed Dec", 6, 0 )} )
)
);

Your wizardry would be greatly appreciated!

Best, ezra