[R] One question on heatmap
Hua
kaixinsjtu at gmail.com
Tue Nov 2 16:50:12 CET 2010
Dear R-helper:
Suppose we have a matrix:
Gene sample1 sample2
Gcnt1 12.0000 52.80000
Max 8.8000 39.10000
Tmem176b 67.9000 304.70000
Shmt2 8.6000 42.40000
Rtn4 11.5000 57.70000
Il17re 7.6000 38.80000
Bclp2 6.2000 32.10000
Mobkl3 4.4000 32.20000
Akr1b10 3.4000 30.10000
Atp6ap2 5.4000 48.20000
Snx2 5.7000 63.10000
Tmem176a 7.6000 91.40000
Klhl9 1.7000 30.30000
Fbxo27 1.0000 28.90000
Scd1 34.6000 0.70000
Tspan9 35.8000 4.20000
2210016L21Rik 39.1000 4.90000
Ctnnb1 212.1000 33.10000
Apoe 397.2000 74.20000
H2-DMb1 72.3000 14.10000
Ryk 31.7000 6.40000
Dapk2 85.4000 17.30000
Gzmm 179.4000 36.80000
Actb 12993.4000 2678.10000
Faim3 758.0000 157.60000
Aktip 209.4000 46.00000
Tbrg1 93.3000 21.30000
When I try to make heatmap based on this gene expression value table, I found that, when I set 'scale' to 'column', the heatmap will be always be red. I think this is because, there's very large values in the matrix (gene Actb), while the most are just very small. Thus, the color will be very ugly. I just wonder, how to set the color to make the heatmap look better? I have tried log-tranformation on the matrix and it's better now. But I do want to know if you have better ways to set the color span manually and make the heatmap look better without any log-transformation?
Thanks in advance!
Best, Hua
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