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Single legend for Hierarchical clustering heat map

shnias83

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

Accepted answers

Chris_Kirchberg

Thanks for the response. Sorry for the confusion, I was refering to the graphic from the journal you shared for fold changes.

You essentially have standarized data already. Standardize Data takes each Y (Column) and subtracts the column mean and divides by the column standard deviation (see below link).

http://www.jmp.com/support/help/13-2/Transformations_to_Y_Columns_Variables.shtml

Since you have normalized RNA-seq results in the same units, then definately uncheck standardize data since they all have the same scale (meaning) per sample for each gene (Y Column) . I am guessing that the normalized FPKM values are also log2 tranformed? You would then have over and under represented genes displayed as postive and negative, respectively, on the scale

I hope that helps.

Chris.

All comments

txnelson

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

shnias83

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.

txnelson

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

shnias83

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.

txnelson

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
);

shnias83

Thanks Jim

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