volcano

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volcano [2019/07/06 12:18]
127.0.0.1 external edit
volcano [2019/07/06 12:18] (current)
tongyifan
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 {{indexmenu_n>​9}} {{indexmenu_n>​9}}
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 ====== Volcano plot ====== ====== Volcano plot ======
  
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 //Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.// //Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.//
  
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 ===== Setting area ===== ===== Setting area =====
  
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 1. It reminds you which kind of plot you are working on. 1. It reminds you which kind of plot you are working on.
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 Volcano plot figures will be shown in this area. Volcano plot figures will be shown in this area.
  
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 A toolbar will show up at the top right of this plotting area when a Volcano plot is created. A toolbar will show up at the top right of this plotting area when a Volcano plot is created.
  
-{{  http://​www.clickgenome.org/​img/​guide/​503.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​503.png?​direct& ​ }}
  
 1. Zoom in: Rectangular zoom in tool. This tool allows you to select a region to display at full application size. After clicking this botton, your mouse will turn into a small cross. Then click and hold the left mouse button and drag a rectangle around a portion of the screen and have it zoom in. 1. Zoom in: Rectangular zoom in tool. This tool allows you to select a region to display at full application size. After clicking this botton, your mouse will turn into a small cross. Then click and hold the left mouse button and drag a rectangle around a portion of the screen and have it zoom in.
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 5 .Data table: If you want to download the sample data in a table, you can click this button. Then a table containing all data will show up in the plotting area like this. You can select and copy the whole table or any part of it into a word or excel file by selecting and clicking right mouse button as you usally do. You can scroll down to see the information of other samples. You also can click the "​close"​ button at the bottom left of this page to close the table page and go back to the default page with the plotting area. 5 .Data table: If you want to download the sample data in a table, you can click this button. Then a table containing all data will show up in the plotting area like this. You can select and copy the whole table or any part of it into a word or excel file by selecting and clicking right mouse button as you usally do. You can scroll down to see the information of other samples. You also can click the "​close"​ button at the bottom left of this page to close the table page and go back to the default page with the plotting area.
  
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 For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding line. For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding line.
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 For example: in the above figure, after putting the mouse on a line, a catalog showed up is: For example: in the above figure, after putting the mouse on a line, a catalog showed up is:
  
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 From the left to the right are: gene symbol and p-value of this gene in the corresponding two cancer types. Therefore, in this example: the gene symbol is PHACTR4, the p-value of its copy number variations in lung adenocarcinoma and lung squmous cell carcinoma tumor samples is 9.32e-15 which means it has significantly different copy number variations in these two groups. From the left to the right are: gene symbol and p-value of this gene in the corresponding two cancer types. Therefore, in this example: the gene symbol is PHACTR4, the p-value of its copy number variations in lung adenocarcinoma and lung squmous cell carcinoma tumor samples is 9.32e-15 which means it has significantly different copy number variations in these two groups.
  
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 ===== Figure downloading and DIY area ===== ===== Figure downloading and DIY area =====
  
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 ==== 1. Figure Downloading area: ==== ==== 1. Figure Downloading area: ====
  • volcano.txt
  • Last modified: 2019/07/06 12:18
  • by tongyifan