mutation-mapper tool

[1191...@zju.edu.cn]

Hi,
We are impressed by your mutation-mapper tool(https://github.com/cBioPortal/mutation-mapper),and we want to quote it in our website,but As shown in the figure below,the functional domain given by the "PFAM Service URL"  is inconsistent with the results of the actual keratin in the PDB database (since keratin is a fibrous protein, only a paragraph-based crystalline structure is currently available),so we want to change it to genomenexus API(eg.https://www.genomenexus.org/ensembl/canonical-transcript/hgnc/KRT1?isoformOverrideSource=uniprot)  as you do in https://www.cbioportal.org/  ,However,we find it hard to alter it to another URL,because other URL needs different request parameters and different parser of the response data.We want to get a more accurate domain annotation,how can we do it or do you provide new javascript version of Mutation Mapper? Thanks.

Best wishes,

 

[Ino de Bruijn]

Hi!

Glad to hear you like the mutation mapper tool!

We have a new version of the standalone tool:

https://github.com/cBioPortal/react-mutation-mapper

Which is the one used here:

https://www.cbioportal.org/mutation_mapper

Hope that helps!

Best wishes,

Ino

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[1191...@zju.edu.cn]

Hi Ino,

Thanks for your pleasant reply.Is there an example or a doc on how to use it in html?

Best wishes,

Ada 

-----原始邮件-----
发件人:"Ino de Bruijn" <i...@ino.pm>
发送时间:2019-09-26 22:40:25 (星期四)
收件人: 1191...@zju.edu.cn
抄送: "cBioPortal for Cancer Genomics Discussion Group" <cbiop...@googlegroups.com>, chenl...@zju.edu.cn
主题: Re: [cbioportal] mutation-mapper tool

[1191...@zju.edu.cn]

Hi Ino,

Sorry to bother you again.When run "npm install --save" on the new version of the mutation-mapper tool,I met the error message(shown in the picture bellow).How to solve the problem?Is there an example or a doc on how to use it in html? Thank you.

Best wishes,

Ada 

 

-----原始邮件-----
发件人:1191...@zju.edu.cn
发送时间:2019-09-27 11:22:56 (星期五)
收件人: "Ino de Bruijn" <i...@ino.pm>

抄送: "cBioPortal for Cancer Genomics Discussion Group" <cbiop...@googlegroups.com>, chenl...@zju.edu.cn

主题: Re: Re: [cbioportal] mutation-mapper tool

[Ino de Bruijn]

Hi Ada,

Thanks for reaching out! One of our engineers is looking into writing some more documentation and will reach out you soon.

Best wishes,

Ino

[Onur Sumer]

Hi Ada, 

react-mutation-mapper is specifically designed to work with react applications. It may not work properly with plain HTML/JS projects. I would suggest creating a new react app by using create-react-app tool: https://github.com/facebook/create-react-app. 

You can then add the library by typing "yarn add react-mutation-mapper". I would also suggest using the latest beta version (yarn add react-muta...@0.3.0-beta.7). Documentation is not ready yet, but minimally you can initialize a mutation mapper component as follows:

import {MutationMapper} from "react-mutation-mapper";

...

...

public render()
{
    return (
        <MutationMapper
            hugoSymbol="BRCA1"
            data={[{
                proteinChange: "L347C",
                proteinPosStart: 347
            }]}
        />
    );
}

...

...

Here proteinPosStart value is critical because that position is actually mapped to the lollipop plot.

Alternatively, you can initialize the mutation mapper with a set of mutations with genomic locations only, and enable annotation with Genome Nexus:

import {MutationMapper} from "react-mutation-mapper";

...

...

public render()
{
    return (
        <MutationMapper
             hugoSymbol="BRCA1"
             filterMutationsBySelectedTranscript={true}
             data={[{
                 chromosome: "17",
                 startPosition: 41246509,
                 endPosition: 41246509,
                 referenceAllele: "G",
                 variantAllele: "-"
             }]}
         />
    );
}

...

...

Please note that currently you need to set filterMutationsBySelectedTranscript to true to enable the annotation. This is a known issue, and we are planning to add an explicit option to enable/disable annotation with Genome Nexus.

Hope this helps.

Best,

Onur

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CAOMQCYEU59nELgpXwXoCNA5rZfUL6RKqzbD4j%3D3xoFC2uwHRCA%40mail.gmail.com.

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[1191...@zju.edu.cn]

Hi Onur,

Thank you for your detailed guidance.I'll try it.If I meet with problems,I may reach out you.Thanks again.

Best,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>
发送时间:2019-10-10 22:45:55 (星期四)
收件人: 1191...@zju.edu.cn
抄送: cbiop...@googlegroups.com, chenl...@zju.edu.cn

[1191...@zju.edu.cn]

Hi Onur,

I tried the react-mutation-mapper with react applications,and get the page shown bellow,it seems that it lost the CSS style,how can I add the style? In addition,can I get the 3D structure which is shown in https://www.cbioportal.org/mutation_mapper?

Best wishes,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>
发送时间:2019-10-10 22:45:55 (星期四)
收件人: 1191...@zju.edu.cn

抄送: cbiop...@googlegroups.com, chenl...@zju.edu.cn

[Li Xiang]

Hi Ada,

Currently we don't have 3D structure in react-mutation-mapper. For the style, you can try to import these CSS files to your project: " import 'react-mutation-mapper/dist/styles.css';" and "import 'react-table/react-table.css';".

Hope this helps.

Best wishes,

Xiang

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/200472e9.21c43.16db9ccf36b.Coremail.11918067%40zju.edu.cn.

[1191...@zju.edu.cn]

Hi Xiang,
OK,thank you.We are looking forward to your full document.
Best wishes,
Ada

[1191...@zju.edu.cn]

Hi Onur,

I have 2 problems,can you help me? 

1.Is there an interface which can choose one mutation by default just as the effect of clicking on a certain mutation in the lollipop line?-the circle on the line in the lollipop enlarged and the table shows only the chosen mutation. (shown as 1.1,1.2,1.3 in the following picture)

2.what does the "Mutation Status" and "ClinVarID" means? how can I custom these fields?(shown as 2 in the following picture)

Thank you.

Best Wishes,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>
发送时间:2019-10-10 22:45:55 (星期四)
收件人: 1191...@zju.edu.cn

抄送: cbiop...@googlegroups.com, chenl...@zju.edu.cn

[1191...@zju.edu.cn]

Hi Xiang,

The table style is Ok,but I still has a problems on the drop-down list style(shown in the picture bellow), how can I correct it?

Thank you.

Best Wishes,

Ada

-----原始邮件-----
发件人:"Li Xiang" <wdx...@gmail.com>
发送时间:2019-10-12 04:24:00 (星期六)
收件人: 1191...@zju.edu.cn
抄送: "Onur Sumer" <s.onur...@gmail.com>, cbiop...@googlegroups.com, chenl...@zju.edu.cn

[Onur Sumer]

Hi Ada,

1) To be able to have an initial selection, you need to set the "selectionFilters" property. For your specific case, you can add a property like this:

selectionFilters={[

    {
        type: DataFilterType.POSITION,
        values: [182]
    }
]}

2) You can customize table columns by using the "mutationTableColumns" property. Here is an example usage: https://github.com/knowledgesystems/msk-insight/blob/218b082aab7d61d9ca07bb06d18fd6e05090b648/client/src/components/MutationMapper.tsx#L134

Hope this helps,

Onur

[Onur Sumer]

Hi Ada,

Reducing the font size for the html element that contains your mutation mapper instance may help solving this problem.

--Onur

On Thu, Oct 24, 2019 at 4:41 AM <1191...@zju.edu.cn> wrote:

[1191...@zju.edu.cn]

Hi Onur,

OK, thank you for your kind answer.I'll try it.

Best wishes,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>
发送时间:2019-10-28 18:27:41 (星期一)
收件人: 1191...@zju.edu.cn
抄送: "Li Xiang" <wdx...@gmail.com>, chenl...@zju.edu.cn, cbiop...@googlegroups.com
主题: Re: Re: Re: [cbioportal] mutation-mapper tool

[1191...@zju.edu.cn]

Hi Onur,

The initial selection was implemented at the lollipop,but the corresponding table rows doesn't change.Is there something I miss?

Best

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>

发送时间:2019-10-28 18:22:57 (星期一)
收件人: 1191...@zju.edu.cn
抄送: chenl...@zju.edu.cn, cbiop...@googlegroups.com

[Onur Sumer]

Hi Ada,

I think the problem is related to the mutation data you are passing to the MutationMapper component. Position filters are currently checking only the proteinPosStart values. Ideally we should also check the protein change values. I'll try to improve that.

For now, as a workaround, can you try adding a proteinPosStart field for each mutation you have? So for example for L475P, proteinPosStart value should be 475. Let me know if this approach works. 

~Onur

[1191...@zju.edu.cn]

Hi Onur,

Thanks for your reply.

Yes,I pass the proteinPosStart value to the MutationMapper component,the data property is like this:'

[{"proteinChange":"K74I","mutationType":"Missense_Mutation","proteinPosStart":"74"},{"proteinChange":"V155G","mutationType":"Missense_Mutation","proteinPosStart":"155"}

...]', for the result,it seems to works the initial selection on the lollipop,but not trigger the table for the change.

Best,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>

发送时间:2019-10-30 21:40:52 (星期三)

收件人: 1191...@zju.edu.cn
抄送: chenl...@zju.edu.cn, cbiop...@googlegroups.com

主题: Re: Re: Re: [cbioportal] mutation-mapper tool

[Onur Sumer]

Hi Ada,

proteinPosStart values should be integer, not string. For example, do proteinPosStart: 74 instead of proteinPosStart: "74". This should fix the initial filter problem.

Best,

Onur

[1191...@zju.edu.cn]

Hi Onur,

Thanks for your reminding,it works!Thank you very much!

Best,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>

发送时间:2019-11-01 15:15:32 (星期五)

收件人: 1191...@zju.edu.cn
抄送: chenl...@zju.edu.cn, cbiop...@googlegroups.com

主题: Re: Re: Re: Re: [cbioportal] mutation-mapper tool

[lulu]

Hi Onur,

Sorry to bother you again. I have three more questions about the mutation-mapper tool shown in the picture bellow.

1.How to hide the tracks options?

2.How to hide the table?

3.How the set the UniProt?

I'm looking forward to your reply.

Best wishes,

Ada 

-----原始邮件-----
发件人:1191...@zju.edu.cn
发送时间:2019-11-01 16:27:47 (星期五)
收件人: "Onur Sumer" <s.onur...@gmail.com>
抄送: chenl...@zju.edu.cn, cbiop...@googlegroups.com
主题: Re: Re: Re: Re: Re: [cbioportal] mutation-mapper tool

[lulu]

Hi,

I have find the way to hide the track option, but I can't find how to hide the table and set the UniProt. Can you help me out? I'm new to react, so I need your help. Thanks. I'm looking forward to hearing from you.

Best wishes,

Ada

-----原始邮件-----
发件人:lulu <lulu...@zju.edu.cn>
发送时间:2020-06-29 14:14:08 (星期一)

收件人: "Onur Sumer" <s.onur...@gmail.com>
抄送: chenl...@zju.edu.cn, cbiop...@googlegroups.com

主题: Re: Re: Re: Re: Re: Re: [cbioportal] mutation-mapper tool

[Onur Sumer]

Hi Ada,

Make sure to upgrade to the latest version of react-muta...@0.6.3. And then use these 2 properties to hide those components: showTrackSelector and mutationTable

So something like this should work:

    showTrackSelector={false}
    mutationTable={<span />}

For the full list of available options take a look at https://github.com/cBioPortal/cbioportal-frontend/blob/97d211b37627ddc9f46d7044d2f4f653db49576c/packages/react-mutation-mapper/src/component/mutationMapper/MutationMapper.tsx#L35

I am assuming that you only provide hugoGeneSymbol in your mutation data. To be able to see the Uniprot Id, you need to provide both entrezGeneId and hugoGeneSymbol in your mutation data.

So your mutation data should look like this:

{

    gene: {

        hugoGeneSymbol: "TP53",

        entrezGeneId: 7157

    },

    chromosome: ...,

    ,,,

}

Hope this helps.

-Onur

[lulu]

Hi Onur,

It works! Thanks for your help.

Best wishes,

Ada

-----原始邮件-----
发件人:"Onur Sumer" <s.onur...@gmail.com>
发送时间:2020-07-22 01:28:16 (星期三)
收件人: lulu <lulu...@zju.edu.cn>
抄送: cbiop...@googlegroups.com, chenl...@zju.edu.cn
主题: Re: Re: Re: Re: Re: Re: Re: [cbioportal] mutation-mapper tool