Inquiry of Heatmap legend (add color legend bar)

[颖孙]

(1) Is it possible to add this kind of legend bar to the Circos heatmaps? 

(I wish to get a bar which could show from white->grey->black)

(2) How can I get the color index which is automatically calculated by Circos for each data point?

I used <rules> shown as follows:

#heatmap

<plot>

type=heatmap

file=/Users/moranlab/circos-0.62-1/Jun_Circos/chr_data/insertionIndex_chr.txt

r0=0.89r

r1=0.99r

#minsize = 1000

<rules>

<rule>

condition=var(value) <= 0

show=no

</rule>

# this rule will remap the value onto a color, using the Brewer

# 9-color blue palette (blues-9-seq-N, N=1..9).

# the remap_round function syntax is

# remap_round(VAR,min,max,remap_min,remap_max)

<rule>

condition=var(value) > 0

color = eval(sprintf("greys-9-seq-%d",remap_round(var(value),0,0.7212911,1,9)))

</rule>

</rules>

</plot>

Thanks a lot!!!!!!

Ying Sun

[颖孙]

As to the second question, I mean:

how can I know what color has been assigned to each data point?

Thank you!!

[Martin Krzywinski]

Circos doesn't create legends right now.

It also doesn't report the association between heat map value and color. I have to add this.

To make a grey heat map, I suggest you use the greys Brewer palette. It's enough to do this in the <plot> block

type = heatmap

color = greys-9-seq

min = 0

max = 100

to map the range [0,100] onto the 9-color Brewer palette. Unless you want to do your own remapping, you don't need to use <rules>. The example you posted was created to illustrate how rules work.

The Brewer palettes don't start/end with white/black. If you want to include them you can add a color to the list

color = white,greys-9-seq,black

though be aware of the fact that this will break the perceptual uniformity of the palette. If you want to assign a specific color to the min/max values, then you can use a rule.

<rules>

<rule>

condition = var(value) == 0

color = white
</rule>

<rule>

condition = var(value) == 100

color = black

</rule>

</rules>

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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