Question

motifStack Plotting the correct data positions on x axis

1

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Marwah • 0

@544f0487

Last seen 2.7 years ago

Australia

Hi all, I'm trying to use motifStack R package to plot amino acid specific positions but analysis but I’m facing a problem with the x axis positions’ titles, the numbers are not equal to the position number that I want. For example, in the photo attached below, the positions are assigned from (1:12) automatically but these are not the positions that I have in my matrix and data sets. How can I change the positions numbers to represents what I want please? Any help is really appreciated!

motifStack R • 1.0k views

ADD COMMENT • link 2.8 years ago Marwah • 0

score 2 · Accepted Answer · 2022-03-14

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Ou, Jianhong ★ 1.3k

@ou-jianhong-4539

Last seen 7 days ago

United States

It will be available in the coming version. You can try to install the development version via my github now

BiocManager::install("jianhong/motifStack")

To change the x-axis, please try:

plot(motif, xaxis=c('your', 'x-axis', 'here', 'please', 'keep', 'same', 'length', 'as', 'the', 'motif'))

Let me know if you have any trouble.

Jianhong.

ADD COMMENT • link 2.8 years ago Ou, Jianhong ★ 1.3k

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Hi Dr. Jianhong, Thank you very much for your reply, its really appreciated!. I tried the code and it worked perfectly!!! thank you again for doing such amazing package! I also have another issue please, I'm plotting amino acid frequency and I want to change the y label to reflect frequencies from 0 to 100 instead of the default option in the package which is from 0 to 1. Can you please help me with this? Many thanks for your help and efforts. Regards Marwah

ADD REPLY • link 2.8 years ago Marwah • 0

1

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Please try to reinstall the development version via the github

BiocManager::install("jianhong/motifStack")

And then try:

plot(motif, ic.scale=c(FALSE, 100))

It is reasonable to change the y-axix as you described. In current stage, I did not have other plan to plot y-axis with user defined values.

Jianhong.

ADD REPLY • link 2.8 years ago Ou, Jianhong ★ 1.3k

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Hi Dr Jianhong, Thank you so much its working now, I really appreciate your help. The Plots looks nice now. Regards Marwah

ADD REPLY • link 2.8 years ago Marwah • 0