ClueGO : will it be possible to display %Genes/term in the pie chart in results of analysis section

[BIOMICS]

Hi All,

While performing CLueGO analysis, in the results of analysis tab under cluster section we can see the bar chart also we have in the x-axis name as %Genes/term. However in the pie chart continuing with it there is no display of % for each category (group). 

I request help if it is possible to display each category (group) name along with the % value for pie chart also. 

Thanks,

Nara

[Bernhard]

Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. So what you want to see is the percentage of the group size compared to the total? We could add also a pie chart that summarizes the total number of unique genes per group.
Best

[Narasimhan Kothandaraman]

Hi Bernhard,  I'm able to see the pie chart. However I like to add % Genes/term for each section in the pie chart. 

Thanks

Nara

On Wednesday, 22 November 2017, 21:38, Bernhard <gabriel...@gmail.com> wrote:

Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. What we could add is a pie chart that summarizes the total number of unique genes per group. Is it that what you want to display?

Best

On Wednesday, November 22, 2017 at 2:05:27 PM UTC+1, BIOMICS wrote:

Hi All,

While performing CLueGO analysis, in the results of analysis tab under cluster section we can see the bar chart also we have in the x-axis name as %Genes/term. However in the pie chart continuing with it there is no display of % for each category (group). 

I request help if it is possible to display each category (group) name along with the % value for pie chart also. 

Thanks,

Nara

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[Bernhard]

Hi Nara, we will add this to our next release.
Best

On Wednesday, November 22, 2017 at 3:28:04 PM UTC+1, BIOMICS wrote:

Hi Bernhard,  I'm able to see the pie chart. However I like to add % Genes/term for each section in the pie chart. 

Thanks

Nara

On Wednesday, 22 November 2017, 21:38, Bernhard <gabriel...@gmail.com> wrote:

Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. What we could add is a pie chart that summarizes the total number of unique genes per group. Is it that what you want to display?
Best

On Wednesday, November 22, 2017 at 2:05:27 PM UTC+1, BIOMICS wrote:

Hi All,

While performing CLueGO analysis, in the results of analysis tab under cluster section we can see the bar chart also we have in the x-axis name as %Genes/term. However in the pie chart continuing with it there is no display of % for each category (group). 

I request help if it is possible to display each category (group) name along with the % value for pie chart also. 

Thanks,

Nara

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[Nara K]

Hi Bernhard,

Thanks

With the available dates is it possible to calculate the % values manually, please let me know.

Regards, Nara 

On 23 Nov 2017 5:46 PM, "Bernhard" <gabriel...@gmail.com> wrote:

Hi Nara, we will add this to our next release.
Best

On Wednesday, November 22, 2017 at 3:28:04 PM UTC+1, BIOMICS wrote:

Hi Bernhard,  I'm able to see the pie chart. However I like to add % Genes/term for each section in the pie chart. 

Thanks

Nara

On Wednesday, 22 November 2017, 21:38, Bernhard <gabriel...@gmail.com> wrote:

Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. What we could add is a pie chart that summarizes the total number of unique genes per group. Is it that what you want to display?
Best

On Wednesday, November 22, 2017 at 2:05:27 PM UTC+1, BIOMICS wrote:

Hi All,

While performing CLueGO analysis, in the results of analysis tab under cluster section we can see the bar chart also we have in the x-axis name as %Genes/term. However in the pie chart continuing with it there is no display of % for each category (group). 

I request help if it is possible to display each category (group) name along with the % value for pie chart also. 

Thanks,

Nara

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[Bernhard]

Hi Nara, I put a latest development version here:
http://www.ici.upmc.fr/cluego-plugin-2.5.1.jar
http://www.ici.upmc.fr/cluepedia-plugin-1.5.1.jar

Just to keep you current files, make copy the folder v2.5.0 to a new folder v.2.5.1 before you install the new plugins (install them from file in the 'App manager' after you downloaded them). This makes sure that you have all your files in the newer version as well. Let me know if it is what you want. The show gene percentage per group pie chart you can toggle using the right mouse button on the graph and select ''Change overview chart ..." see down the screen shot.

Best

On Thursday, November 23, 2017 at 11:46:44 AM UTC+1, BIOMICS wrote:

Hi Bernhard,

Thanks

With the available dates is it possible to calculate the % values manually, please let me know.

Regards, Nara 

On 23 Nov 2017 5:46 PM, "Bernhard" <gabriel...@gmail.com> wrote:

Hi Nara, we will add this to our next release.
Best

On Wednesday, November 22, 2017 at 3:28:04 PM UTC+1, BIOMICS wrote:

Hi Bernhard,  I'm able to see the pie chart. However I like to add % Genes/term for each section in the pie chart. 

Thanks

Nara

On Wednesday, 22 November 2017, 21:38, Bernhard <gabriel...@gmail.com> wrote:

Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. What we could add is a pie chart that summarizes the total number of unique genes per group. Is it that what you want to display?
Best

On Wednesday, November 22, 2017 at 2:05:27 PM UTC+1, BIOMICS wrote:

Hi All,

While performing CLueGO analysis, in the results of analysis tab under cluster section we can see the bar chart also we have in the x-axis name as %Genes/term. However in the pie chart continuing with it there is no display of % for each category (group). 

I request help if it is possible to display each category (group) name along with the % value for pie chart also. 

Thanks,

Nara

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[Narasimhan Kothandaraman]

Hi Bernhard,

It perfectly worked. Many thanks

Nara

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[Narasimhan Kothandaraman]

Hi Bernhard, 

Just to clarify, the asterisk sign (**) marks next to the % values in the pie chart does it indicates the p-values. Is it correct to say the following if indicates the p-values? 

Single (*) or double (**) asterisk indicate significant enriched GO terms at the p < 0.05 and p < 0.01 statistical levels, respectively. 

On another note even if I don't select "Show only pathways with pV <_ 0.05", the asterisk sign appears in the pie chart. Is it independent of the selection? 

Please clarify. 

Thank you,

Nara

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[Bernhard]

Hi Nara,

On Wednesday, March 7, 2018 at 6:37:01 PM UTC+1, BIOMICS wrote:

Hi Bernhard, 

Just to clarify, the asterisk sign (**) marks next to the % values in the pie chart does it indicates the p-values. Is it correct to say the following if indicates the p-values? 

Single (*) or double (**) asterisk indicate significant enriched GO terms at the p < 0.05 and p < 0.01 statistical levels, respectively. 

Yes this is correct.

On another note even if I don't select "Show only pathways with pV <_ 0.05", the asterisk sign appears in the pie chart. Is it independent of the selection? 

 Yes it is independent of the selection.

Please clarify. 

Thank you,

Nara

Best

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[Narasimhan Kothandaraman]

Many thanks, Bernhard.

Nara

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[ca...@miamioh.edu]

Good to clarify. Is there anybody know what is this pie chart based on (percentage of which)? Or if I can revise the figure (pie chart on biological process, attached) to remove some of the non-significant terms as the labels are squeezed and cannot read? Thanks,

Jingyi

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[Narasimhan Kothandaraman]

Yes, I too had a similar issue recently where I had to squeeze nearly 28 terms in a CluePedia pie chart. If there is a way to reduce this to less than 10 it would be very useful from a visualization purpose of the data and say we are only showing only 10 out of 20 significant "% of genes per term" or relevant details of the pie chart. 

Many thanks,

Nara

---

From: "ca...@miamioh.edu" <ca...@miamioh.edu>
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Saturday, 24 March 2018, 3:26
Subject: Re: [cytoscape-helpdesk] Re: ClueGO : will it be possible to display %Genes/term in the pie chart in results of analysis section

Good to clarify. Is there anybody know what is this pie chart based on (percentage of which)? Or if I can revise the figure (pie chart on biological process, attached) to remove some of the non-significant terms as the labels are squeezed and cannot read? Thanks,

Jingyi

On Wednesday, March 7, 2018 at 12:37:01 PM UTC-5, BIOMICS wrote:

Hi Bernhard, 

Just to clarify, the asterisk sign (**) marks next to the % values in the pie chart does it indicates the p-values. Is it correct to say the following if indicates the p-values? 

Single (*) or double (**) asterisk indicate significant enriched GO terms at the p < 0.05 and p < 0.01 statistical levels, respectively. 

On another note even if I don't select "Show only pathways with pV <_ 0.05", the asterisk sign appears in the pie chart. Is it independent of the selection? 

Please clarify. 

Thank you,

Nara

On Thursday, 23 November 2017, 7:48:49 PM GMT+8, Bernhard <gabriel...@gmail.com> wrote:

Hi Nara, I put a latest development version here:

http://www.ici.upmc.fr/cluego- plugin-2.5.1.jar
http://www.ici.upmc.fr/ cluepedia-plugin-1.5.1.jar

To view this discussion on the web visit https://groups.google.com/d/ msgid/cytoscape-helpdesk/ 21d6ee34-5c48-4da5-ab6c- b13eec96b008%40googlegroups. com.

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[Bernhard]

Hi, the only way to have a smaller pie chart at the moment is to run a more restrictive analysis so that you end up with less groups and only the most significany terms. The pie and the label size can be changed by clicking on the right mouse button an in/decrease the size.
Best

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[ca...@miamioh.edu]

Thanks Bernhard! One more question, would you know how to export the pie chart figure in a higher resolution?

Best,

Jingyi

[Bernhard]

Hi Jingyi, if you click on the right mouse button on the image you should get the option to save the image as svg, so you can scale it afterwards as large as you want.
Best

[emilian...@gmail.com]

Il giorno mercoledì 22 novembre 2017 14:38:08 UTC+1, Bernhard ha scritto:
> Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. So what you want to see is the percentage of the group size compared to the total? We could add also a pie chart that summarizes the total number of unique genes per group.
> Best

Dear Bernhard, I really liked the possibility to add the % in the pie charts; however, it is still not clear to me how this value is calculated.

I would indeed like to see the percentage of unique genes in each group compared to the total input genes number. However, at the moment, this value does not seem to be calculated in that way and I can't figure out what it truely represents.

Thank you very much for your help,
Emiliano.

[Bernhard]

Hi Emiliano,

please see bellow an example calculation for the pie chart with the number of genes for a ClueGO-CluePedia term-gene network. Please note that shared genes between groups are included in each of the groups.

Let us know if you have other questions.

Best

Le mercredi 1 août 2018 01:24:12 UTC+2, Emiliano Dalla a écrit : > Il giorno mercoledì 22 novembre 2017 14:38:08 UTC+1, Bernhard ha scritto: > > Hi Nara, the overview pie chart shown at the moment summarizes the number of terms per group. So what you want to see is the percentage of the group size compared to the total? We could add also a pie chart that summarizes the total number of unique genes per group. > > Best > > Dear Bernhard, I really liked the possibility to add the % in the pie charts; however, it is still not clear to me how this value is calculated. > > I would indeed like to see the percentage of unique genes in each group compared to the total input genes number. However, at the moment, this value does not seem to be calculated in that way and I can't figure out what it truely represents. > > Thank you very much for your help, > Emiliano.