Single legend for Hierarchical clustering heat map

[#1]

Hi,

Thanks in advance for the support!

I'm making a Heatmap using 'two way clustering' in the hierarchical cluster. When I add the legend to the figure, it gives me one legend per column. I would like to have only one legend (color code) for the whole heatmap. I appreciate your guidance on that. 

Shahram

[#2]

If you select the "Scale Uniformly" check box on the Cell Plot dialog box, you will only get one legend when you select it.

[#3]

Thanks for the reply.

I'm not using Cell Plot though.

As I want a heatmap combined with a dendrogram, I'm doing a cluster analysis through: Alnalyze > Clustering > Hierarchical cluster.

There's no such an option, Scale Uniformly, in the clustering dialog.

[#4]

If you Unselect the "Standardize Data" the legend will only have 1 copy displayed

[#5]

Yes, that's correct.

However, unselecting 'Standardize Data' will change the clutering pattern and column ordering. So I will get a different heatmap which dosen't convey my mesage clearly. 

[#6]

Treating your data a Distance Matrix, will also result in a common legend.  The multiple legends are being displayed, because every column has a different range, thus a separate legend.  If you just want to get rid of all of the legends except one, the code below will illustrate how to do that....but I am not sure that is what you want to do.

Names Default To Here( 1 );
dt = Open( "$SAMPLE_DATA\Drosophila Aging Distances.jmp" );

hc = Hierarchical Cluster(
	Y(
		:ORE_FEMALE_WK1_1,
		:ORE_FEMALE_WK1_2,
		:ORE_FEMALE_WK1_11,
		:ORE_FEMALE_WK1_12,
		:ORE_FEMALE_WK1_21,
		:ORE_FEMALE_WK1_24,
		:ORE_FEMALE_WK6_1,
		:ORE_FEMALE_WK6_2,
		:ORE_FEMALE_WK6_11,
		:ORE_FEMALE_WK6_12,
		:ORE_FEMALE_WK6_21,
		:ORE_FEMALE_WK6_24,
		:ORE_MALE_WK1_3,
		:ORE_MALE_WK1_4,
		:ORE_MALE_WK1_9,
		:ORE_MALE_WK1_10,
		:ORE_MALE_WK1_19,
		:ORE_MALE_WK1_20,
		:ORE_MALE_WK6_3,
		:ORE_MALE_WK6_4,
		:ORE_MALE_WK6_9,
		:ORE_MALE_WK6_10,
		:ORE_MALE_WK6_19,
		:ORE_MALE_WK6_20,
		:SAM_FEMALE_WK1_7,
		:SAM_FEMALE_WK1_8,
		:SAM_FEMALE_WK1_15,
		:SAM_FEMALE_WK1_16,
		:SAM_FEMALE_WK1_22,
		:SAM_FEMALE_WK1_23,
		:SAM_FEMALE_WK6_7,
		:SAM_FEMALE_WK6_8,
		:SAM_FEMALE_WK6_15,
		:SAM_FEMALE_WK6_16,
		:SAM_FEMALE_WK6_22,
		:SAM_FEMALE_WK6_23,
		:SAM_MALE_WK1_5,
		:SAM_MALE_WK1_6,
		:SAM_MALE_WK1_13,
		:SAM_MALE_WK1_14,
		:SAM_MALE_WK1_17,
		:SAM_MALE_WK1_18,
		:SAM_MALE_WK6_5,
		:SAM_MALE_WK6_6,
		:SAM_MALE_WK6_13,
		:SAM_MALE_WK6_14,
		:SAM_MALE_WK6_17,
		:SAM_MALE_WK6_18
	),
	Label( :Observation ID ),
	Method( "Ward" ),
	Standardize Data( 1 ),
	Legend( 1 ),
	Dendrogram Scale( "Distance Scale" ),
	Number of Clusters( 5 ),
	Color Map( "Blue to Gray to Red" ),
	SendToReport( Dispatch( {}, "Dendrogram", OutlineBox, {SetHorizontal( 1 )} ) )
);


For( i = 48, i > 1, i--,
	Report( hc )[Table Box( i )] << delete
);

[#7]

Thanks Jim

I have attached a figure from a paper which has used JMP. I want to replicate that if possible.

[#8]

What version of JMP are you using?

I'm having difficulty visualizing the multiple legends that you're getting.

Can you share a picture of what you're getting?

If not, can you reproduce the situation with one of the sample data sets (Help->Sample Data and search for "Cluster")?

Here's what I can get with the Cereal data.

[#9]

Jeff,

To see the multiple legends, take the script that I included above, using the Drosophila Aging Distances data, but remove the For loop that deletes the multiple legends.

JIm

[#10]

Thanks, Jim. I'm going to blame that on Monday morning fog in my brain. ;-) Yes, if I turn on Standardize Data in the Clustering launch dialog and get a Color Map and a Legend then I get this with the Cereal data.

@shnias83, notice that I have to have multiple legends because the colors mean different things for each column because the data has been standardized. You said that you want the standardization because it gives you the analysis and visualization you need. What legend would you use since the colors have different values for each column?