Fill Color Mapping Help

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tyler.fr...@gmail.com

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Apr 12, 2019, 2:52:14 PM4/12/19
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Hello,

I am trying to apply what I learned about using Fill Color mapping in the tutorial to help express certain aspects of my data, however I am having a bit of trouble. When I select 'Fill Color' and then 'Mapping' I then go to select a gene like in the tutorial and only three options show up: Name, Selected, Selected Name. There is no option for choosing one of my genes and then I cannot choose continuous mapping, how can I fix this? This also raises a second question, how do I go about choosing the gene for the column section? I have Excel Microarray results that have fold change as well as p-value. Do I choose the gene with the highest p-value or fold change? Any help would be greatly appreciated as I am quite new to both Cytoscape and Microarray analysis. Thank you in advance!

Tyler

Alex Pico

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Apr 12, 2019, 3:12:26 PM4/12/19
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Hi Tyler,

Fill Color (and other visual properties) have three fields: Default, Mapping and Bypass. The Mapping field is for selecting a column of data and “mapping” it to a visual property. For example, if you had a range of numerical values associated with each gene, then you could map those numbers to Fill Color.  If you are wanting to control the color of a single gene, then you want the “Bypass” field. This will let you set the Fill Color for a single gene directly.

After loading you excel data into Cytoscape, then that column (e.g., “log2fc” or whatever you named it in Excel) will show up in the Node Table and it will then also show up in the “Mapping” options.

You can always refer to the material at tutorials.cytoscape.org for a refresher;

These topics are also covered in the manual:

And we even have a YouTube video on using color palettes for Node Fill Color mappings that I recommend:

Cheers,
 - Alex



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tyler.fr...@gmail.com

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Apr 12, 2019, 7:34:00 PM4/12/19
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Hey Alex,

Thank you for the response, I really appreciate your dedication to such a great program. In terms of my data input, I actually uploaded it to String-DB, the webpage, first and then downloaded that as a tab delimited file and uploaded that to Cytoscape. Also, I followed this video: https://www.youtube.com/watch?v=oNxXxyVQfrk for uploading the data from String-DB into a SIF file format. Which one is preferred in this scenario? As well, my fold change column does not show up when they are put into either of the aforementioned file forms, both from String-DB directly and from creating a SIF file myself. How can I go about getting my data into the right format to where I can almost mirror the tutorial on Basic Data Visualization? Thanks again for your assistance.

Tyler

Alex Pico

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Apr 12, 2019, 8:50:24 PM4/12/19
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Why aren’t you using the STRING app for Cytoscape? You can paste your query into Cytoscape and get a STRING network and all the associate node and edge attributes into Cytoscape with a single step!

 - Alex



tyler friedman

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Apr 12, 2019, 8:55:02 PM4/12/19
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I have in fact downloaded and used the String app! I just imported my data using the methods I had mentioned earlier, so I didn’t think there was much of a point to go back to the String app. Unless I would be able to apply the same filters/parameters to the data/PPI that the app gave me? As in that would allow me to follow the tutorial that I had mentioned in order to isolate the most effected pathway. If you could elaborate a bit more based on my questions that’d be great, I am really trying to get a whole wealth of knowledge on microarray analysis! 

Thank you, 

Tyler 



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Scooter Morris

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Apr 18, 2019, 10:58:54 AM4/18/19
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Hi Tyler,
   You should be able to import your fold change data (File->Import->Table from file) into your stringApp network.   The tricky part is to make sure to match a column from the STRING network (typically you would use "query term") to the column in your table that has the same identifiers.  Then you should see a new column in the node table with your fold change data.  Then you should be able to set up a continuous mapping for color.

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Hey Alex,

Thank you for the response, I really appreciate your dedication to such a great program. In terms of my data input, I actually uploaded it to String-DB, the webpage, first and then downloaded that as a tab delimited file and uploaded that to Cytoscape. Also, I followed this video: https://www.youtube.com/watch?v=oNxXxyVQfrk for uploading the data from String-DB into a SIF file format. Which one is preferred in this scenario? As well, my fold change column does not show up when they are put into either of the aforementioned file forms, both from String-DB directly and from creating a SIF file myself. How can I go about getting my data into the right format to where I can almost mirror the tutorial on Basic Data Visualization? Thanks again for your assistance.

Tyler 

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tyler.fr...@gmail.com

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Apr 18, 2019, 3:43:54 PM4/18/19
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> Thank you for the response, I really appreciate your dedication to such a great program. In terms of my data input, I actually uploaded it to String-DB, the webpage, first and then downloaded that as a tab delimited file and uploaded that to Cytoscape. Also, I followed this video: https://www.youtube.com/watch?v=oNxXxyVQfrk for uploading the data from String-DB into a SIF file format. Which one is preferred in this scenario? As well, my fold change column does not show up when they are put into either of the aforementioned file forms, both from String-DB directly and from creating a SIF file myself. How can I go about getting my data into the right format to where I can almost mirror the tutorial on Basic Data Visualization? Thanks again for your assistance.
>
> Tyler 
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Hey Scooter,

Thank you for the reply! When I went to import my data from excel, I chose two columns (Fold change and Gene Symbol; which is what I put into String) by clicking the 'not imported' button when hovering over the column title. When I went to import them, there were no values present for the columns I had just chosen to add to the current table. If it helps, the data is directly from the TAC program by Applied Biosystems from ThermoFisher, only copied into an excel document. Also, when you told me I had to match one of my columns from my data to one from the String Network, I was not too sure how to go about doing that. If you could elaborate or point in the direction of some sort of tutorial that would be great. Thanks again for the reply!

-Tyler

ssbsm...@gmail.com

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Apr 25, 2019, 10:46:40 AM4/25/19
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Hi Tyler,
    You can take a look at the tutorial here: https://cytoscape.org/cytoscape-tutorials/protocols/stringApp/#/ particularly Exercise #2.  It goes through an example step-by-step of how to import data from String using the stringApp and then merging in additional data from a separate file.

-- scooter
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> Thank you for the response, I really appreciate your dedication to such a great program. In terms of my data input, I actually uploaded it to String-DB, the webpage, first and then downloaded that as a tab delimited file and uploaded that to Cytoscape. Also, I followed this video: https://www.youtube.com/watch?v=oNxXxyVQfrk for uploading the data from String-DB into a SIF file format. Which one is preferred in this scenario? As well, my fold change column does not show up when they are put into either of the aforementioned file forms, both from String-DB directly and from creating a SIF file myself. How can I go about getting my data into the right format to where I can almost mirror the tutorial on Basic Data Visualization? Thanks again for your assistance.
>
> Tyler 
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tyler friedman

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Apr 26, 2019, 9:48:31 AM4/26/19
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Hi Scooter, 

I took a look at the tutorial you linked and it is exactly what I am looking for! Just one small problem. My data comes from ThermoFisher's TAC software and so I do not have UniProt IDs for my genes and the resulting Excel files from the software do not look like the example files that are used in the tutorial. Any way you could help me with formatting the data from TAC into viable excel sheets that can uploaded and used for the tutorial? Thank you for your continued help.

Tyler

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> Thank you for the response, I really appreciate your dedication to such a great program. In terms of my data input, I actually uploaded it to String-DB, the webpage, first and then downloaded that as a tab delimited file and uploaded that to Cytoscape. Also, I followed this video: https://www.youtube.com/watch?v=oNxXxyVQfrk for uploading the data from String-DB into a SIF file format. Which one is preferred in this scenario? As well, my fold change column does not show up when they are put into either of the aforementioned file forms, both from String-DB directly and from creating a SIF file myself. How can I go about getting my data into the right format to where I can almost mirror the tutorial on Basic Data Visualization? Thanks again for your assistance.
>
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Hey Scooter,

Thank you for the reply! When I went to import my data from excel, I chose two columns (Fold change and Gene Symbol; which is what I put into String) by clicking the 'not imported' button when hovering over the column title. When I went to import them, there were no values present for the columns I had just chosen to add to the current table. If it helps, the data is directly from the TAC program by Applied Biosystems from ThermoFisher, only copied into an excel document. Also, when you told me I had to match one of my columns from my data to one from the String Network, I was not too sure how to go about doing that. If you could elaborate or point in the direction of some sort of tutorial that would be great. Thanks again for the reply!

-Tyler

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ssbsm...@gmail.com

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May 2, 2019, 11:47:06 AM5/2/19
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Can you provide the column headers?  STRING doesn't really care if you use UniProt IDs or Gene Symbols -- if you follow the tutorial and substitute "Gene Symbol" anywhere it wants "UniProt IDs" the results should be roughly the same.

-- scooter
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> Thank you for the response, I really appreciate your dedication to such a great program. In terms of my data input, I actually uploaded it to String-DB, the webpage, first and then downloaded that as a tab delimited file and uploaded that to Cytoscape. Also, I followed this video: https://www.youtube.com/watch?v=oNxXxyVQfrk for uploading the data from String-DB into a SIF file format. Which one is preferred in this scenario? As well, my fold change column does not show up when they are put into either of the aforementioned file forms, both from String-DB directly and from creating a SIF file myself. How can I go about getting my data into the right format to where I can almost mirror the tutorial on Basic Data Visualization? Thanks again for your assistance.
>
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Hey Scooter,

Thank you for the reply! When I went to import my data from excel, I chose two columns (Fold change and Gene Symbol; which is what I put into String) by clicking the 'not imported' button when hovering over the column title. When I went to import them, there were no values present for the columns I had just chosen to add to the current table. If it helps, the data is directly from the TAC program by Applied Biosystems from ThermoFisher, only copied into an excel document. Also, when you told me I had to match one of my columns from my data to one from the String Network, I was not too sure how to go about doing that. If you could elaborate or point in the direction of some sort of tutorial that would be great. Thanks again for the reply!

-Tyler

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