How to put highlighted text just above the points?

[YiweiNiu]

Hi Lilin,

Thanks very much for developing this useful tool.

I wonder if there is a way to add highlighed text labels right on top of the points, like this one.

Thank you in advance.

Bests, Yiwei

[YinLiLin]

Hi Yiwei,

I am not sure if it can address your issue, please try to add two parameters in CMplot, like: highlight.text.yadj=rep(1, length(N_ht)), highlight.text.xadj=rep(0, length(N_ht)), where N_ht is the number of highlighted SNPs.

Regards, Lilin

[YiweiNiu]

Hi Lilin,

Thank you for your quick reply. I tried this method, but it did not work.

In highlight.text.yadj=rep(1, length(N_ht)), highlight.text.xadj=rep(0, length(N_ht)), N_ht should be the highlighted SNPs?

Otherwise it would throw an error like:

Error in highlight_text(x = pvalue.posN[highlight_index[[i]]], y = logpvalue[highlight_index[[i]]], : length of xadj not equals to length of x

Bests, Yiwei

[YinLiLin]

Sorry for the unclear statement, it should be rep(1, N_ht) or rep(1, length(ht). This setting only helps to initialize the start positions of labels around the highlighted points, however, if there are too many highlighted SNPs, the positions will be changed to generate non-overlapped layout.

[YiweiNiu]

Hi Lilin,

Thanks a lot for your prompt reply. There were about six SNPs I wanted to highlight. Using highlight.text.yadj = rep(1, N_ht), highlight.text.xadj = rep(0, N_ht) could not generate the plot I pasted above. Maybe I will use AI to modify the final plot.

Thank you.

[JingjingBai2021]

Hi Lilin,

I am wondering if the highlight.text.xadj function has been removed in the latest version of CMplot.

Is there any ways to change the position of all highlighted text in the figure?

I found the plot that I generated recently is not the same with the previous one.

Is it possible to change the color of line between the signal and highlight text and also the line type?

[JingjingBai2021]

I solved the issue by sourcing the old version CMplot. But to be honest, the function highlight.text.xadj makes the figure look nicer and I strongly suggest to add them into the latest version.:)

[YinLiLin]

Hi Jingjing,

Thank you for the question. Yes, the relevant parameters have been removed from the latest version, because i found it not that flexible and may be rarely used in actual situations. Anyway, i will take your suggestions into consideration in the next new update.

Best, LL

[xiduo111]

I solved the issue by sourcing the old version CMplot. But to be honest, the function highlight.text.xadj makes the figure look nicer and I strongly suggest to add them into the latest version.:)

Hi Jingjing, which version did you use, I just have the same problem

[JingjingBai2021]

I downloaded the old version:CMplot_4.2.0.tar.gz.

Best, Jingjing

Sent from Outlook for iOShttps://aka.ms/o0ukef

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From: Xi Duo @.> Sent: Thursday, January 25, 2024 2:33:43 PM To: YinLiLin/CMplot @.> Cc: Bai, J (mdl) @.>; Comment @.> Subject: Re: [YinLiLin/CMplot] How to put highlighted text just above the points? (Issue #68)

I solved the issue by sourcing the old version CMplot. But to be honest, the function highlight.text.xadj makes the figure look nicer and I strongly suggest to add them into the latest version.:)

Hi Jingjing, which version did you use, I just have the same problem

— Reply to this email directly, view it on GitHubhttps://github.com/YinLiLin/CMplot/issues/68#issuecomment-1910231473, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYTHG6F64BVIIH665YNU5ADYQJNLPAVCNFSM5TSAP5YKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOJRGAZDGMJUG4ZQ. You are receiving this because you commented.Message ID: @.***>

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[xiduo111]

I downloaded the old version:CMplot_4.2.0.tar.gz. Best, Jingjing Sent from Outlook for iOShttps://aka.ms/o0ukef … ____ From: Xi Duo @.> Sent: Thursday, January 25, 2024 2:33:43 PM To: YinLiLin/CMplot @.> Cc: Bai, J (mdl) @.>; Comment @.> Subject: Re: [YinLiLin/CMplot] How to put highlighted text just above the points? (Issue #68) I solved the issue by sourcing the old version CMplot. But to be honest, the function highlight.text.xadj makes the figure look nicer and I strongly suggest to add them into the latest version.:) Hi Jingjing, which version did you use, I just have the same problem — Reply to this email directly, view it on GitHub<#68 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYTHG6F64BVIIH665YNU5ADYQJNLPAVCNFSM5TSAP5YKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOJRGAZDGMJUG4ZQ. You are receiving this because you commented.Message ID: @.***> ____ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

Thanks a lot, I will try it.