What about more than 100 Species?

[Z1997B]

Dear tanghaibao,

Thank you for developing such a good collinearity tool. I realize that you set the Y-axis length of the mcsan_layout file for your drawing to 1, which is handy when there are less than 10 species. However, when my number of species exceeds 10 or even reaches 100, I cannot reasonably assign the Y-axis to 100 species. The resulting image shows chromosomes squeezed together. Can you give me some advice on collinear mapping of chromosomes in a large number of species?

Many thanks,
Bo Zhang

[tanghaibao]

@Z1997B

The range for y-axis is 1, however, you can use a float value to position the tracks. It's all relative.

I have not tried more than 10 species but it may still be possible. For example, you can use --figsize=20x20 (default is 8x7) to have a bigger canvas to draw. Then the tracks will appear smaller relative to the canvas size.

Finally, even if you have more than 10 species, you can specify, in the layout file, to only display certain pairs of tracks (a.b.anchors.simple, b.c.anchors.simple, ...), under the edges section (e).

https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)

[Z1997B]

@tanghaibao I do try to use a float value to position the tracks. Thanks for your response~

[MR-D-CJ]

@Z1997B

The range for y-axis is 1, however, you can use a float value to position the tracks. It's all relative.

I have not tried more than 10 species but it may still be possible. For example, you can use --figsize=20x20 (default is 8x7) to have a bigger canvas to draw. Then the tracks will appear smaller relative to the canvas size.

Finally, even if you have more than 10 species, you can specify, in the layout file, to only display certain pairs of tracks (a.b.anchors.simple, b.c.anchors.simple, ...), under the edges section (e).

https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)

How to modify this parameter--figsize=20x20

[tanghaibao]

@MR-D-CJ

Just use larger figure size --figsize=20x20 means 20 inches wide and 20 inches high. --dpi=300 (default) means dot per inch is 300, so in terms of pixels, it is 6000x6000, leading to higher resolution. If you use --format=pdf (default) it doesn't really matter in terms of resolution, since it is vector graphics anyways and you can easily scale the image and not lose resolution.

Sometimes we also change the --figsize if we need to have a fat image, say --figsize=10x5 will give a height half than the width (e.g. we have lots of genes on a horizontal track).

Since font size stay unchanged by default, a bigger figure size make the labels appear smaller, as a side effect.

[chosyang]

Dear tanghaibao,

Thank you for developing such a good collinearity tool. I realize that you set the Y-axis length of the mcsan_layout file for your drawing to 1, which is handy when there are less than 10 species. However, when my number of species exceeds 10 or even reaches 100, I cannot reasonably assign the Y-axis to 100 species. The resulting image shows chromosomes squeezed together. Can you give me some advice on collinear mapping of chromosomes in a large number of species?

Many thanks, Bo Zhang

Can you tell me the command for suppose 5 species please. I'm struggling to make inputs and command even after going thorugh readme file as I m new to this