analyze_yours_mountain

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
analyze_yours_mountain [2019/07/06 13:06]
127.0.0.1 external edit
analyze_yours_mountain [2019/07/06 13:08] (current)
Line 1: Line 1:
 +{{indexmenu_n>​13}}
 +
 ====== Analyze yours: Mountain plot ====== ====== Analyze yours: Mountain plot ======
  
Line 31: Line 33:
 //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.//
  
-{{  http://​www.clickgenome.org/​img/​guide/​900.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​900.png?​direct& ​ }}
  
-{{  http://​www.clickgenome.org/​img/​guide/​901.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​901.png?​direct& ​ }}
  
 ===== Setting area ===== ===== Setting area =====
Line 41: Line 43:
 2. You can upload your data in a file through the dialog box here. Only '​xlsx'​ file is acceptable. Please make sure all data are in the first sheet of this file. If there are more than one group of samples, please put them into separate files. 2. You can upload your data in a file through the dialog box here. Only '​xlsx'​ file is acceptable. Please make sure all data are in the first sheet of this file. If there are more than one group of samples, please put them into separate files.
  
-{{  http://​www.clickgenome.org/​img/​guide/​902.png?​nolink&​30%}}+{{  http://​www.clickgenome.org/​img/​guide/​902.png?​nolink& ​ }}
  
 3. You need to specify the datatype here to tell us how to do log transformation (for mRNA expression values, it's log2 transformation;​ for CNV (copy number variation) values, it's log2(CNV/2) transformation). 3. You need to specify the datatype here to tell us how to do log transformation (for mRNA expression values, it's log2 transformation;​ for CNV (copy number variation) values, it's log2(CNV/2) transformation).
Line 63: Line 65:
 Mountain plot figures will be shown in this area. Mountain plot figures will be shown in this area.
  
-{{  http://​www.clickgenome.org/​img/​guide/​903.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​903.png?​direct& ​ }}
  
 A toolbar will show up at the top right of this plotting area when a Mountain plot is created. A toolbar will show up at the top right of this plotting area when a Mountain plot is created.
  
-{{  http://​www.clickgenome.org/​img/​guide/​904.png?​nolink&​30%}}+{{  http://​www.clickgenome.org/​img/​guide/​904.png?​nolink& ​ }}
  
 1. Zoom in: Rectangular zoom in tool. This tool allows you to select a region to display at full application size. After selecting 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 zoomed in. 1. Zoom in: Rectangular zoom in tool. This tool allows you to select a region to display at full application size. After selecting 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 zoomed in.
Line 83: Line 85:
 → Horizontally zoom in: Slide the mouse wheel (for apple magic mouse, slide up or down) up or down, you can zoom in or zoom out horizontally. → Horizontally zoom in: Slide the mouse wheel (for apple magic mouse, slide up or down) up or down, you can zoom in or zoom out horizontally.
  
-{{  http://​www.clickgenome.org/​img/​guide/​905.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​905.png?​direct& ​ }}
  
 For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding marker. For your convinence, the sample ID and other details of each individual gene will show up when you put your mouse on the corresponding marker.
  
-{{  http://​www.clickgenome.org/​img/​guide/​906.png?​nolink&​30%}}+{{  http://​www.clickgenome.org/​img/​guide/​906.png?​nolink& ​ }}
  
 For example: in the above figure, aftering putting the mouse on a marker, a catalog showed up is: For example: in the above figure, aftering putting the mouse on a marker, a catalog showed up is:
Line 95: Line 97:
 ♦ Second row: x-axis, y-axis, gene symbol ♦ Second row: x-axis, y-axis, gene symbol
  
-Δ  x-axis: start location of the concern gene in the corresponding chromosome;+Δ x-axis: start location of the concern gene in the corresponding chromosome;
  
-Δ  y-axis: median/mean mRNA expression, copy number variation values depends on which data type you are working on;+Δ y-axis: median/mean mRNA expression, copy number variation values depends on which data type you are working on;
  
-Δ  gene symbol: a symbol provided in your uploaded file.+Δ gene symbol: a symbol provided in your uploaded file.
  
 Therefore, in this example: the gene symbol is LCE3C, its start location in chromosome 7 is 152573137 and the mean value of its copy number variations in group 1 is 2.793. Therefore, in this example: the gene symbol is LCE3C, its start location in chromosome 7 is 152573137 and the mean value of its copy number variations in group 1 is 2.793.
Line 105: Line 107:
 ===== Figure downloading and DIY area ===== ===== Figure downloading and DIY area =====
  
-{{  http://​www.clickgenome.org/​img/​guide/​907.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​907.png?​direct& ​ }}
  
 ==== 1.Figure Downloading area: ==== ==== 1.Figure Downloading area: ====
Line 123: Line 125:
 Only '​xlsx'​ file type is acceptable! The default sheet is the first sheet of each '​*.xlsx'​ file. This area shows the table format for you to arrange your data. You also can download the example files and use them to try the functions provided in this page. Only '​xlsx'​ file type is acceptable! The default sheet is the first sheet of each '​*.xlsx'​ file. This area shows the table format for you to arrange your data. You also can download the example files and use them to try the functions provided in this page.
  
-{{  http://​www.clickgenome.org/​img/​guide/​908.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​908.png?​direct& ​ }}
  
 → Please make sure that per group per '​*.xlsx'​ file. → Please make sure that per group per '​*.xlsx'​ file.
Line 139: Line 141:
 You may not like the colors and sizes of the markers plotted in default. Therefore, you can use the Figure DIY options to change the color, size and shapes of markers. You may not like the colors and sizes of the markers plotted in default. Therefore, you can use the Figure DIY options to change the color, size and shapes of markers.
  
-{{  http://​www.clickgenome.org/​img/​guide/​909.png ​ }}+{{  http://​www.clickgenome.org/​img/​guide/​909.png?​direct& ​ }}
  
  
  • analyze_yours_mountain.txt
  • Last modified: 2019/07/06 13:08
  • (external edit)