beeswarm_plot_by_gene

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beeswarm_plot_by_gene [2019/07/06 08:55]
tongyifan created
beeswarm_plot_by_gene [2019/07/06 13:02] (current)
tongyifan
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-====== Bee-swarm ​plot_By Gene ======+{{indexmenu_n>​4}} 
 + 
 +====== Bee-swarm ​plot by gene ======
  
 In this webpage, you can create Bee-swarm plots of the distributions of a specific gene in samples across different cancer types. In this webpage, you can create Bee-swarm plots of the distributions of a specific gene in samples across different cancer types.
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 As we mentioned above, there are three ways to get into the Bee-swarm plot_By Gene page. As we mentioned above, there are three ways to get into the Bee-swarm plot_By Gene page.
  
-1) Through the Navigation bar at the Home page, select "​Bee-swarm ​plot _ By Gene" under "Data Analysis";​+1) Through the Navigation bar at the Home page, select "​Bee-swarm ​plot_By ​Gene" under "Data Analysis";​
  
 2) Go to "Data Analysis"​ page, then go to "Data visualization"​ area, select "​Bee-swarm plot _ By Gene" under Bee-swarm plot area; 2) Go to "Data Analysis"​ page, then go to "Data visualization"​ area, select "​Bee-swarm plot _ By Gene" under Bee-swarm plot area;
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 3) Through the link in the "Link area" at the Home page, go to "Data Analysis"​ page, then go to "Data visualization"​ area, select "by gene" at the bottom of Bee-swarm plot area. 3) Through the link in the "Link area" at the Home page, go to "Data Analysis"​ page, then go to "Data visualization"​ area, select "by gene" at the bottom of Bee-swarm plot area.
  
-For '​Bee-swarm ​plot _ By Gene' page, there are five areas:+{{ youtube>​Ut2z8TMjRwg?​large }} 
 + 
 +For '​Bee-swarm ​plot_By ​Gene' page, there are five areas:
  
-{{http://​www.clickgenome.org/​img/​guide/​01.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​01.png?​nolink&​824x893  ​}}
  
 ===== Overview ===== ===== Overview =====
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 → Link area: Necessary links are available for you to switch to other pages or websites. → Link area: Necessary links are available for you to switch to other pages or websites.
  
-//Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.// ===== Setting area =====+//Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.// 
 +===== Setting area =====
  
-{{http://​www.clickgenome.org/​img/​guide/​02.png?​nolink&​30%}}+{{  http://​www.clickgenome.org/​img/​guide/​02.png?​nolink&​325x508  ​}}
  
 1. It reminds you which kind of bee-swarm plot you are working on. 1. It reminds you which kind of bee-swarm plot you are working on.
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 ♦ For two cutoff values, if cutoff1 > cutoff2, then ♦ For two cutoff values, if cutoff1 > cutoff2, then
  
-∇   ​percentages of ≥ cutoff1+∇ percentages of ≥ cutoff1
  
-∇   ​percentages of ≥ cutoff2 and < cutoff1+∇ percentages of ≥ cutoff2 and < cutoff1
  
-∇   ​percentages of < cutoff2 \\+∇ percentages of < cutoff2\\
 will be calculated and shown in the plotting area beside the corresponding bee-swarm plots. will be calculated and shown in the plotting area beside the corresponding bee-swarm plots.
  
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 Bee-swarm figures will be plotted in this area as follows. Bee-swarm figures will be plotted in this area as follows.
  
-{{http://​www.clickgenome.org/​img/​guide/​03.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​03.png?​nolink&​906x427  ​}}
  
 A toolbar will show up at the top right of this plotting area when Bee-swarm plots are created. A toolbar will show up at the top right of this plotting area when Bee-swarm plots are created.
  
-{{http://​www.clickgenome.org/​img/​guide/​04.png?​nolink&​30%}}+{{  http://​www.clickgenome.org/​img/​guide/​04.png?​nolink&​191x97  ​}}
  
 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.
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 5. Data table: If you want to download the sample data, you can click this button. Then a table containing all data will show up in the plotting area like this: 5. Data table: If you want to download the sample data, you can click this button. Then a table containing all data will show up in the plotting area like this:
  
-{{http://​www.clickgenome.org/​img/​guide/​05.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​05.png?​nolink&​872x725  ​}}
  
 The first part of this table shows the usefull statistics of the samples, then the value and sample ID of each individual case in each group. You can select and copy the whole table or any part of it into a word or excel file by clicking and holding right mouse button as you usally do. The first part of this table shows the usefull statistics of the samples, then the value and sample ID of each individual case in each group. You can select and copy the whole table or any part of it into a word or excel file by clicking and holding right mouse button as you usally do.
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 For your convinence, the sample ID and other details of each individual sample will show up when you put your mouse on the corresponding marker. For example: in the following figure, aftering putting the mouse on a marker, a catalog showed up is: For your convinence, the sample ID and other details of each individual sample will show up when you put your mouse on the corresponding marker. For example: in the following figure, aftering putting the mouse on a marker, a catalog showed up is:
  
-{{http://​www.clickgenome.org/​img/​guide/​06.png?​nolink&​30%}}+{{  http://​www.clickgenome.org/​img/​guide/​06.png?​nolink&​370x66  ​}}
  
 ♦ First row: the group message of this sample; ♦ First row: the group message of this sample;
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 ♦ Second row: x-axis, y-axis, sample ID: ♦ Second row: x-axis, y-axis, sample ID:
  
-Δ  x-axis: calculated from a program to separate samples in a bee-swarm like plot, no biological meaning;+Δ x-axis: calculated from a program to separate samples in a bee-swarm like plot, no biological meaning;
  
-Δ  y-axis: mRNA expression, copy number variation values depends on which data type you are working on;+Δ y-axis: mRNA expression, copy number variation values depends on which data type you are working on;
  
-Δ  sample ID: for the data provided by our website which were downloaded from TCGA/GDC public portal, it was given by GDC portal; for your own data, you can name your own sample ID.+Δ sample ID: for the data provided by our website which were downloaded from TCGA/GDC public portal, it was given by GDC portal; for your own data, you can name your own sample ID.
  
 Therefore, in this example: the sample ID is TCGA-06-0187-01,​ and it's mRNA expression value of EGFR in Glioblastoma multiforme is 86384.59375. Therefore, in this example: the sample ID is TCGA-06-0187-01,​ and it's mRNA expression value of EGFR in Glioblastoma multiforme is 86384.59375.
  
-{{http://​www.clickgenome.org/​img/​guide/​07.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​07.png?​nolink&​970x587  ​}}
  
 ===== Figure downloading and DIY area ===== ===== Figure downloading and DIY area =====
  
-{{http://​www.clickgenome.org/​img/​guide/​08.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​08.png?​nolink&​845x210  ​}}
  
 ==== 1. Figure Downloading area: ==== ==== 1. Figure Downloading area: ====
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 **Example 1**: Plotting Bee-swarm of mRNA expression values of EGFR in lung adenocarcinoma tumor samples and calculate the percentages of samples between 1000 and 2000. See below: **Example 1**: Plotting Bee-swarm of mRNA expression values of EGFR in lung adenocarcinoma tumor samples and calculate the percentages of samples between 1000 and 2000. See below:
  
-{{http://​www.clickgenome.org/​img/​guide/​09.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​09.png?​nolink&​972x662  ​}}
  
 In this figure, two cutoff values are given: 1000 and 2000. According to the digital figures in the plot, we can get to know that for EGFR mRNA expression values in lung adenocarcinoma cancer, the percentages are In this figure, two cutoff values are given: 1000 and 2000. According to the digital figures in the plot, we can get to know that for EGFR mRNA expression values in lung adenocarcinoma cancer, the percentages are
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 The parameters in the Setting area are as the following picture. The default setting for the shapes, colors and sizes of markers, boxes and mean lines for all groups are the same. The parameters in the Setting area are as the following picture. The default setting for the shapes, colors and sizes of markers, boxes and mean lines for all groups are the same.
  
-{{http://​www.clickgenome.org/​img/​guide/​010.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​010.png?​nolink&​970x614  ​}}
  
 **Example 3**:​Plotting Bee-swarms of mRNA expression values of gene KRAS in glioblastoma multiforme, esophageal carcinoma and lung adenocarcinoma tumor samples and do the t-test between esophageal carcinoma and lung adenocarcinoma tumor samples. **Example 3**:​Plotting Bee-swarms of mRNA expression values of gene KRAS in glioblastoma multiforme, esophageal carcinoma and lung adenocarcinoma tumor samples and do the t-test between esophageal carcinoma and lung adenocarcinoma tumor samples.
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 The p value shown in the figure is 2.56e-6 which means in these two cancer types, the KRAS mRNA expression is significantly different. The p value shown in the figure is 2.56e-6 which means in these two cancer types, the KRAS mRNA expression is significantly different.
  
-{{http://​www.clickgenome.org/​img/​guide/​012.png?​nolink&​80%}}+{{  http://​www.clickgenome.org/​img/​guide/​012.png?​nolink&​972x581  ​}}
  
  
  • beeswarm_plot_by_gene.1562403335.txt.gz
  • Last modified: 2019/07/06 08:55
  • by tongyifan