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What is an UpSet diagram?
It can be said to be a variant of the Venn diagram. For the visualization of collective data, it is suitable for a small number of groups of data sets. It is generally used for gene intersection analysis of transcriptome data. Recently, I found the same pattern when analyzing metabolome data of different groups. Reasoning, let’s take my own data as an example, the rendering is as follows:
UpSet chart online analysis website
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What I use directly here is Lianchuan Bio Cloud Platform , Cloud Tools-Search-UpSet Picture
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Download official sample files to prepare data
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The column name is the name of the gene (in my example, it is the name of the metabolite), and the row name is the name of the sample group. If the sample detects the column name, the corresponding position is marked as "1", otherwise it is "0". See below for details. data preparation
data preparation
- The website has specific video tutorials , but in short, the names of substances identified in all groups are combined into one column. If each group contains the substance, it will be recorded as 1, and if it does not, it will be recorded as 0. Here is an example: I want to make Upset plot of differential metabolites identified in Rumen, Serum and Milk
- Column A is the union of differential metabolites identified in Rumen, Serum, and Milk. F/G/H is the differential metabolites identified in Rumen, Serum, and Milk respectively. The current goal is if column F and column A overlap . For the data, mark "1" in column B n
=IF(COUNTIF(F:F,A2)=0,"1","0"). For example, search for (+/-)12(13)-DiHOME of A2. If the substance exists in Rumen, use the formula and pull down the same column (more for two columns) For the formula of repeated data, you can refer to the comparison of the two columns of data in the Excel table to find out the similarities and differences )
- After all the data is found, copy B/C/D and re-paste it, select
仅粘贴数值and delete columns F/G/H, and then save and upload the website for analysis.
Generate results plots and adjustments
But let’s not go into details. The left 参数调整area can set the font size, graphic size, coordinate axis, etc., and the right side supports exporting PNG/PDF/SVG/TIFF and other formats. You can adjust the image size and download the intersection data. The effect is already in the header. Given, you can explore more by yourself