Analyze yours: Bee-swarm plot

In this webpage, you can create Bee-swarm plots of the distributions of your own data. There are two ways to get into the Bee-swarm plot page.

1) Through the Navigation bar at the Home page, select “Bee-swarm plot” under “Analyze yours”;

2) Go to “Analyze yours” page, select “Bee-swarm plot”;

For 'Bee-swarm plot' page, there are six areas:

→ Navigation bar: You can switch to other pages through this navigation bar.

→ Setting area: You can upload your data and set up the cutoff values and other parameters here.

→ Plotting area: Bee-swarm plot will be shown in this area.

→ Figure Downloading and DIY area: You can download Mountain plot in certain format and size. You can also customize line color, line shape, marker color, and marker shapes through the option buttons in this area.

→ Example area: An example of the upload file is given here. You can download it through the link.

→ 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.

1. It reminds you which kind of plot you are working on.

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.

3. You can specify statistical options here.

→ Log2: by checking this box, log2 transformation will be applied to the data before Bee-swarm plot (for mRNA expression values, it's log2 transformation; for CNV (copy number variation) values, it's log2(CNV/2) transformation).

→ boxplot: by checking this box, a boxplot will shown together with bee-swarm plot for each group of samples.

→ mean: by checking this box, a line with shown together with the mean value of each group of samples.

→ mean±std: by checking this box, two lines with shown together with the mean value of mean+std and mean-std each group of samples.

→ mean±2std: by checking this box, two lines with shown together with the mean value of mean+2std and mean-2std each group of samples. 2std means 2 times of the standard deviation of a group of samples

→ mean±3std: by checking this box, two lines with shown together with the mean value of mean+3std and mean-3std each group of samples. 3std means 3 times of the standard deviation of a group of samples.

4. When bee-swarms of more than one groups of samples are plotted, unpaired two-tailed Student's significance test can be calculated when you input the group number here. Note: the group number starts from 1 from the left group to the right.

5. You can input cutoff values here, then the percentage of samples compared with cutoffs will show up in the figures.

For one cutoff value, percentages of samples whose values larger and equal (≥) than it and of ones whose values smaller than it will be calculated.

For two cutoff values, if cutoff1 > cutoff2, then

∇ percentages of ≥ cutoff1

∇ percentages of ≥ cutoff2 and < cutoff1

∇ percentages of < cutoff2
will be calculated and shown in the plotting area beside the corresponding bee-swarm plots.

After setting all these necessary parameters, click “GO” button at the bottom of this area, the Bee-swarms will be plotted in the plotting area. There are no limits on how many groups you want to plot. But due to the configuration of your computer, the internet speed and the data sizes need to be transmitted for plotting (several times of the sample sizes), it may take a while to transmit and to load the data for plotting. The more groups you want to plot, the longer the response time it will cost.

Bee-swarm figures will be plotted in this area as follows.

A toolbar will show up at the top right of this plotting area when Bee-swarm plots are created.

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.

2. Zoom out: Zoom back to the status it was a step before by cliking it.

3. Restore: Show the plots in the original portion.

4. 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.

Vertically zoom in: There is a zoom bar at the right edge of the plotting area. Click and hold on either one of the two buttons on it, you can zoom in or zoom out vertically.

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.

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:

♦ First row: the group message of this sample;

♦ 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 y-axis: the values in your uploaded table;

Δ sample ID: the sample IDs in your uploaded table.

Select the group whose style you want to modify, then modify the color, shape of the markers, box, static lines here.

You can specify image format (png or jpg) and size/dimensions for the image to download .

You can modify color, shape and other details of this figure for you own style.

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 file and use it to try the functions provided in this page.

→ There are MUST be two columns for each group. The first column is consisted of the values of the samples in this group and the second one is consisted of their corresponding IDs. If there is more than one group, the first two columns are for the first group, the second two columns are for the second group, and so on.

→ As what has been mentioned above, the details of sample will show up when you put your mouse on a specific one. Therefore, the sample ID is necessary information. If you don't have any sample ID, PLEASE number them as their IDs and put them on the second column.

→ It not necessary for each group to have the same number of samples which means the sample sizes of all groups are not necessary to be same to each other.

In this figure, two cutoff values are given: 12 and 6. According to the digital figures in the plot, we can get to know that for the uploaded data, the percentages are

≥12: group 1, 5.8%; group 2, 3.46%

<6 and ≥12: group 1, 92.46%; group 2, 96.54%

<6: group 1, 1.74%; group 2, 0%

To make it easier to distinguish groups by a glance, you can use the Figure DIY options to change the color, size and shape of markers.

The p value shown in the figure is 5.68e-16 which means in samples in these two groups are significantly different.

  • analyze_yours_beeswarm.txt
  • Last modified: 2019/07/06 15:05
  • by tongyifan