manhattan

Differences

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

Link to this comparison view

Both sides previous revision Previous revision
manhattan [2019/07/06 12:06]
127.0.0.1 external edit
manhattan [2019/07/06 12:20] (current)
tongyifan
Line 2: Line 2:
  
 ====== Manhattan plot ====== ====== Manhattan plot ======
- 
-{{youtube>​kh41FX8Z-Tg}} 
  
 Normally, for instance in genome-wide association studies (GWAS), a Manhattan plot is a type of scatter plot, usually used to display data with a large number non-zero amplitude data-points. It gains its name from the similarity of such a plot to the Manhattan skyline. In GWAS Manhattan plots, genomic coordinates are displayed along the X-axis. The negative logarithm of the association P-value for each single nucleotide polymorphism (SNP) are displayed on the Y-axis. Therefore, the stronger the associations between SNP, the larger the Y-axis value. Normally, for instance in genome-wide association studies (GWAS), a Manhattan plot is a type of scatter plot, usually used to display data with a large number non-zero amplitude data-points. It gains its name from the similarity of such a plot to the Manhattan skyline. In GWAS Manhattan plots, genomic coordinates are displayed along the X-axis. The negative logarithm of the association P-value for each single nucleotide polymorphism (SNP) are displayed on the Y-axis. Therefore, the stronger the associations between SNP, the larger the Y-axis value.
Line 18: Line 16:
  
 → Besides regular Manhattan plot, we provided another option to show more information in this plot: Directional Manhattan plot. If the median value of the gene in group is smaller than that in group2, the corresponding line points down from the base line (normally, it's zero line). → Besides regular Manhattan plot, we provided another option to show more information in this plot: Directional Manhattan plot. If the median value of the gene in group is smaller than that in group2, the corresponding line points down from the base line (normally, it's zero line).
 +
 +{{ youtube>​kh41FX8Z-Tg }}
  
 ===== Overview ===== ===== Overview =====
Line 43: Line 43:
 //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/​300.png}}+{{http://​www.clickgenome.org/​img/​guide/​300.png?​direct&​}}
  
 ===== Setting area ===== ===== Setting area =====
Line 59: Line 59:
 ❌: not available which means neither tumor samples nor non-malignant samples of this cancer type are available for the data type specified in (4) and (5). ❌: not available which means neither tumor samples nor non-malignant samples of this cancer type are available for the data type specified in (4) and (5).
  
-{{http://​www.clickgenome.org/​img/​guide/​301.png}}+{{http://​www.clickgenome.org/​img/​guide/​301.png?​direct&​}}
  
 4. You can specify the first group here by selecting the cancer type through the drop-down list and the sample type by checking one of the circles. 4. You can specify the first group here by selecting the cancer type through the drop-down list and the sample type by checking one of the circles.
Line 91: Line 91:
 A toolbar will show up at the top right of this plotting area when a Manhattan plot is created. A toolbar will show up at the top right of this plotting area when a Manhattan plot is created.
  
-{{http://​www.clickgenome.org/​img/​guide/​302.png}}+{{http://​www.clickgenome.org/​img/​guide/​302.png?​direct&​}}
  
 1. Save as Image: You can click it to swich into a image saving webpage then click right mouse button to save this image. You also can specify the image format and size by selecting the options in the Figure downloading and DIY area. 1. Save as Image: You can click it to swich into a image saving webpage then click right mouse button to save this image. You also can specify the image format and size by selecting the options in the Figure downloading and DIY area.
Line 97: Line 97:
 2. 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. 2. 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.
  
-{{http://​www.clickgenome.org/​img/​guide/​303.png}}+{{http://​www.clickgenome.org/​img/​guide/​303.png?​direct&​}}
  
-{{http://​www.clickgenome.org/​img/​guide/​304.png}}+{{http://​www.clickgenome.org/​img/​guide/​304.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 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.
Line 105: Line 105:
 For example: in the above figure, after putting the mouse on a line, a catalog showed up like this: For example: in the above figure, after putting the mouse on a line, a catalog showed up like this:
  
-{{http://​www.clickgenome.org/​img/​guide/​305.png}}+{{http://​www.clickgenome.org/​img/​guide/​305.png?​direct&​}}
  
 From the left to the right are: gene symbol and p-value of this gene in the corresponding two groups. Therefore, in this example: the gene symbol is FUDC3B, the p-value of it's copy number variations in lung adenocarcinoma and lung squmous cell carcinoma is 1.36e-95 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 groups. Therefore, in this example: the gene symbol is FUDC3B, the p-value of it's copy number variations in lung adenocarcinoma and lung squmous cell carcinoma is 1.36e-95 which means it has significantly different copy number variations in these two groups.
  
-{{http://​www.clickgenome.org/​img/​guide/​306.png}}+{{http://​www.clickgenome.org/​img/​guide/​306.png?​direct&​}}
  
 ===== Figure downloading and DIY area ===== ===== Figure downloading and DIY area =====
  
-{{http://​www.clickgenome.org/​img/​guide/​307.png}}+{{http://​www.clickgenome.org/​img/​guide/​307.png?​direct&​}}
  
 ==== 1. Figure Downloading area: ==== ==== 1. Figure Downloading area: ====
Line 127: Line 127:
 **Example 1**: Plotting Manhattan plot of copy numbers on chromosome 3 in lung adenocarcinoma tumor vs non-malignant samples with 0.05 as the cutoff of p-value. **Example 1**: Plotting Manhattan plot of copy numbers on chromosome 3 in lung adenocarcinoma tumor vs non-malignant samples with 0.05 as the cutoff of p-value.
  
-{{http://​www.clickgenome.org/​img/​guide/​308.png}}+{{http://​www.clickgenome.org/​img/​guide/​308.png?​direct&​}}
  
 From the figure above, we can see that the whole P-arm genes whose copy number variations in lung adenocarcinoma tumor samples and non-malignant samples are significantly different. On the contrary, only 60.43% of the genes on Q-arm are significantly different. From the figure above, we can see that the whole P-arm genes whose copy number variations in lung adenocarcinoma tumor samples and non-malignant samples are significantly different. On the contrary, only 60.43% of the genes on Q-arm are significantly different.
Line 133: Line 133:
 After checking the Directional Manhattan box, the figure will turn out to be: After checking the Directional Manhattan box, the figure will turn out to be:
  
-{{http://​www.clickgenome.org/​img/​guide/​309.png}}+{{http://​www.clickgenome.org/​img/​guide/​309.png?​direct&​}}
  
 The whole P-arm genes' lines are pointing down which means the lung adenocarcinoma tumor samples has a smaller median copy number variation than that of the corresponding non-malignant samples. From the corresponding Mountain plot, we can see that there is a mild deletion in P-arm which confirms the results we observed above. The whole P-arm genes' lines are pointing down which means the lung adenocarcinoma tumor samples has a smaller median copy number variation than that of the corresponding non-malignant samples. From the corresponding Mountain plot, we can see that there is a mild deletion in P-arm which confirms the results we observed above.
  
-{{http://​www.clickgenome.org/​img/​guide/​310.png}}+{{http://​www.clickgenome.org/​img/​guide/​310.png?​direct&​}}
  
 **Example 2**: Plotting Manhattan plot of copy number variations on chromosome 3 of lung adenocarcinoma tumor samples vs lung squamous cell carcinoma tumor samples with SOX2 and TP63 highlighted. **Example 2**: Plotting Manhattan plot of copy number variations on chromosome 3 of lung adenocarcinoma tumor samples vs lung squamous cell carcinoma tumor samples with SOX2 and TP63 highlighted.
  
-{{http://​www.clickgenome.org/​img/​guide/​311.png}}+{{http://​www.clickgenome.org/​img/​guide/​311.png?​direct&​}}
  
 We can see there are two lines are highlighted in a different color. When we put and hold our mouse on it, the corresponding information will show up. We can see there are two lines are highlighted in a different color. When we put and hold our mouse on it, the corresponding information will show up.
  
-{{http://​www.clickgenome.org/​img/​guide/​312.png}}+{{http://​www.clickgenome.org/​img/​guide/​312.png?​direct&​}}
  
 You may want to know which group has a higher copy number variation median value and you may not like the colors plotted in default. Therefore, you can select the "​Directional Manhattan"​ option and use the Figure DIY options to change the color. The Setting area and the final plot are shown in the following picture. You may want to know which group has a higher copy number variation median value and you may not like the colors plotted in default. Therefore, you can select the "​Directional Manhattan"​ option and use the Figure DIY options to change the color. The Setting area and the final plot are shown in the following picture.
  
-{{http://​www.clickgenome.org/​img/​guide/​313.png}}+{{http://​www.clickgenome.org/​img/​guide/​313.png?​direct&​}}
  
  
  • manhattan.txt
  • Last modified: 2019/07/06 12:20
  • by tongyifan