How to create histogram format not in genetic format

[Lee]

Hi, Everyone. I am beginner of Circos and glad to use this wonderful service!

However, I cannot implement any output histogram or heatmap to my result.

In base data.txt format :

    <variable>    <name>             <start><end>   <color>

chr - var1   Chem_Descriptor1          0 1              lpred

In histogram.txt format : 

<variable> <start><end><values>

hs1  0    0.01 5.00000

hs1  0.02 0.03 7.00000

hs1  0.04 0.05 34.00000

hs1  0.06 0.07 84.00000

hs1  0.08 0.09 192.00000

hs1  0.10 0.11 392.00000

hs1  0.12 0.13 307.00000

hs1  0.14 0.15 283.00000

hs1  0.16 0.17 277.00000

hs1  0.18 0.19 202.00000

hs1  0.20 0.21 164.00000

hs1  0.22 0.23 159.00000

hs1  0.24 0.25 163.00000

hs1  0.26 0.27 162.00000

hs1  0.28 0.29 161.00000

hs1  0.30 0.31 119.00000

hs1  0.32 0.33 155.00000

hs1  0.34 0.35 96.00000

hs1  0.36 0.37 93.00000

hs1  0.38 0.39 70.00000

hs1  0.40 0.41 88.00000

hs1  0.42 0.43 57.00000

hs1  0.44 0.45 59.00000

hs1  0.46 0.47 35.00000

hs1  0.48 0.49 25.00000

hs1  0.50 0.51 20.00000

hs1  0.52 0.53 21.00000

hs1  0.54 0.55 12.00000

hs1  0.56 0.57 5.00000

hs1  0.58 0.59 5.00000

hs1  0.60 0.61 3.00000

hs1  0.62 0.63 2.00000

hs1  0.64 0.65 0.00000

hs1  0.66 0.67 1.00000

hs1  0.68 0.69 1.00000

hs1  0.70 0.71 2.00000

hs1  0.72 0.73 2.00000

hs1  0.74 0.75 2.00000

hs1  0.76 0.77 1.00000

hs1  0.78 0.79 0.00000

hs1  0.80 0.81 0.00000

hs1  0.82 0.83 0.00000

hs1  0.84 0.85 1.00000

hs1  0.86 0.87 0.00000

hs1  0.88 0.89 1.00000

hs1  0.90 0.91 2.00000

hs1  0.92 0.93 0.00000

hs1  0.94 0.95 0.00000

hs1  0.96 0.97 0.00000

hs1  0.98 0.99 1.00000

I want to know what is the problem of implementation to data format and give me a tip to make a text file to create histogram or heatmap!

Thank you!

ps. I already studied about the guide or tutorial(off/online) but still no respond to my result .

[Martin]

Circos requires that position values be integers -- you're using floating point. The integer requirement comes from the fact that the original design was for sequence, where positions are discrete (bases).

Define your "chromosome" like this

chr - x x 0 100 black

This is equivalent to how an actual chromosome might be defined, e.g.

chr - hs1 1 0 249250621 chr1

except now we have

x = name of axis

x = label on axis (you can remove this from the display if you like)

0 = start

100 = end

black = color of axis

Now your data would look like this

x 0 1 5.00

x 2 3 7.00

x 4 5 35.00

...

Note that start-end of the position must be at least 1. The histogram value itself (35.00) can be a floating point number.

m

[S Jin Lee]

Sorry for the late response! However, thank you for your perfect explanation!

Now, I can clearly build the histogram! 

Thank you for your help!

2021년 7월 8일 (목) 오전 4:23, Martin <martin.k...@gmail.com>님이 작성:

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