如何解决 Circos SVG 错误放置文本的问题？
我有以下 Circos 图，我将其渲染为 SVG 文件，然后转换为 PNG，为了便于说明：
围绕外缘的文本标签的方向正确，从 12 点钟到 9 点钟点钟方向，向外，远离灰色弧线。
在 9 和 12 之间，文本标签向内，与灰色弧线重叠。这是预料之外的。
这是一个特写镜头，用于澄清问题：
如果我从 Circos 输出 PNG，而不是 SVG ，标签绘制正确，但随后我无法在 Adobe Illustrator 或 Inkscape 中标记矢量格式的 SVG 图形。所以我需要 SVG 输出。
以下是与添加标签相关的 circos.conf 文件的片段：
<image>
dir = /tmp
file = circos.png
png = yes
radius = 3000p
background = white
angle_offset = -176
</image>
...
<plots>
<plot>
type = text
color = black
file = factorList.txt
r0 = 1r
r1 = 1r+200p
label_size = 12p
label_font = condensedbold
padding = 0p
rpadding = 0p
label_snuggle = yes
max_snuggle_distance = 1r
snuggle_sampling = 2
snuggle_tolerance = 0.25r
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 2p
snuggle_refine = yes
</plot>
</plots>
我不确定可以应用哪些其他选项来尝试解决此问题。我的问题是：我应该在这个或另一个配置文件中尝试什么来修复 SVG 输出？谢谢你的建议。
I have the following Circos diagram, which I rendered as an SVG file and then converted to PNG, for the purposes of illustration:
The text labels that circle the outer rim are oriented correctly from 12 o'clock to 9 o'clock, oriented outwards, away from the grey arcs.
Between 9 and 12, the text labels are oriented inwards, overlapping the grey arc. This is not expected.
Here's a close-up, to clarify the issue:
If I output a PNG from Circos, instead of SVG, the labels are drawn correctly, but then I lose the ability to mark up the vector-formatted SVG figure in Adobe Illustrator or Inkscape. So I need the SVG output.
Here's a snippet of the circos.conf file relevant to the addition of the labels:
<image>
dir = /tmp
file = circos.png
png = yes
radius = 3000p
background = white
angle_offset = -176
</image>
...
<plots>
<plot>
type = text
color = black
file = factorList.txt
r0 = 1r
r1 = 1r+200p
label_size = 12p
label_font = condensedbold
padding = 0p
rpadding = 0p
label_snuggle = yes
max_snuggle_distance = 1r
snuggle_sampling = 2
snuggle_tolerance = 0.25r
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 2p
snuggle_refine = yes
</plot>
</plots>
I'm not sure what other options I can apply to try to resolve this. My question is: What should I try in this or another configuration file, which fixes the SVG output? Thanks for your advice.
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也许你可以尝试这个选项：
我认为上面的布局是由 snuggle 选项引起的，还要检查你的conf文件并确保plot(type=text)的所有“r0”和“r1”都大于1r。
这是 circos 课程示例
Maybe you can try this option:
And I think the layout above caused by the snuggle option ,and also check your conf file and be sure all the "r0" and "r1" of plot(type=text) are bigger than 1r .
Here is the circos lessonss example