Re: [circos] Stacked histogram not depicting all values

[Martin Krzywinski]

I can't reproduce this error. I've attached the image from my end and all the files used to create it. Are you using the latest version?

Note that you probably want

min = 0

max = 100

to control the histogram range. Normally, if not provided, these values are computed from the min/max of the data, but with stacked histograms it can get wonky.

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Mon, Feb 13, 2017 at 6:13 AM, Fayne <vdwa...@gmail.com> wrote:

Hello,

I' m trying to make stacked histograms on 14 different regions. However, there seems to be a problem with axis 8 (chrp53 in the png) because it doesn' t show the last value (17.6 in this case). It just fills the whole histograms with the first 2 values. I don' t have a problem with any of the other axis.

axis1   100     900     82.4,0,17.6

axis2   100     900     64.7,5.9,29.4

axis3   100     900     64.7,0,35.3

axis4   100     900     82.4,5.9,11.8

axis5   100     900     52.9,35.3,11.8

axis6   100     900     76.5,17.6,5.9

axis7   100     900     70.6,17.6,11.8

axis8   100     900     35.3,47.1,17.6

axis9   100     900     76.5,11.8,11.8

axis10  100     900     82.4,5.9,11.8

axis11  100     900     82.4,11.8,5.9

axis12  100     900     82.4,0,17.6

axis13  100     900     64.7,17.6,17.6

axis14  100     900     64.7,17.6,17.6

I' ve already tried retyping or reformatting the files, but it doesn' t fix the problem. It might be a coincidence, but for all the other axis the first value is the biggest ... except for axis 8. Switching sort_bin_values on or off doesn' t fix it either. 

<<include etc/colors_fonts_patterns.conf>>

<<include ideogram.conf>>

<image>

<<include etc/image.conf>>

</image>

karyotype = data/NV_karyotype.txt

<ideogram>

<spacing>

default = 40u

</spacing>

line_color = white

show_label = yes

label_font = default

label_radius = 1r + 85p

label_size = 48

label_parallel = yes

</ideogram>

<plots>

<plot>

file = data/20170213_fig1_small.txt

type = histogram

r0 = 0.6r

r1 = 1.0r

fill_color = green,red,blue

sort_bin_values = no

</plot>

</plots>

<<include etc/housekeeping.conf>>

I' ve added the karyotype file, histogram file and the circos.conf file. Any idea how to fix this problem? 

Thanks in advance!

Kind regards,

Fayne

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