beeswarm_plot_by_cancer

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beeswarm_plot_by_cancer [2019/07/06 11:58]
tongyifan
beeswarm_plot_by_cancer [2019/07/06 12:59] (current)
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 In this webpage, you can create Bee-swarm plots of the distributions of different genes in different samples in one cancer type. In this webpage, you can create Bee-swarm plots of the distributions of different genes in different samples in one cancer type.
  
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 As we mentioned above, there are three ways to get into the '​Bee-swarm plot_By Cancer'​ page. As we mentioned above, there are three ways to get into the '​Bee-swarm plot_By Cancer'​ page.
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 For '​Bee-swarm plot_By Cancer'​ page, there are five areas: For '​Bee-swarm plot_By Cancer'​ page, there are five areas:
  
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 ===== Overview ===== ===== Overview =====
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 ===== Setting area ===== ===== Setting area =====
  
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 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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 Bee-swarm figures will be shown in this area. Bee-swarm 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 Bee-swarm plots are created. A toolbar will show up at the top right of this plotting area when Bee-swarm plots are created.
  
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 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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 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. 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 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:
  
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 → First row: the group message of this sample; → First row: the group message of this sample;
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 Therefore, in this example: the sample ID is TCGA-53-7624-01,​ and it's mRNA expression value of EGFR in Glioblastoma multiforme is 19967.61133. Therefore, in this example: the sample ID is TCGA-53-7624-01,​ and it's mRNA expression value of EGFR in Glioblastoma multiforme is 19967.61133.
  
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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: ====
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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, modify the marker into red diamond. 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, modify the marker into red diamond. See below:
  
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 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 Setting area are shown 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 Setting area are shown 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.
  
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 To make it easier to distinguish groups by a glance, you can use the Figure DIY options to change the color, size and shapes of markers. To make it easier to distinguish groups by a glance, you can use the Figure DIY options to change the color, size and shapes of markers.
  
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 **Example 3**: Plotting Bee-swarms of mRNA expression values of gene CPSF3L and KRAS in both lung adenocarcinoma tumor and non-malignant samples and do the t-test between CPSF3L and KRAS tumor samples. **Example 3**: Plotting Bee-swarms of mRNA expression values of gene CPSF3L and KRAS in both lung adenocarcinoma tumor and non-malignant samples and do the t-test between CPSF3L and KRAS tumor samples.
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 Because CPSF3L and KRAS tumor samples are the second and forth groups from the left, separately. Therefore input 2 and 4 in T-Test input boxes, then click '​GO'​. The p-value as what is shown in the figure is: 0.567 which means their mRNA expression values in lung adenocarcinoma tumor samples are not significantly different. Because CPSF3L and KRAS tumor samples are the second and forth groups from the left, separately. Therefore input 2 and 4 in T-Test input boxes, then click '​GO'​. The p-value as what is shown in the figure is: 0.567 which means their mRNA expression values in lung adenocarcinoma tumor samples are not significantly different.
  
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  • beeswarm_plot_by_cancer.1562414325.txt.gz
  • Last modified: 2019/07/06 11:58
  • by tongyifan