UpSet Plots¶

UpSet plot will show the relation between different sets.

How to use¶

Data upload¶

1. Upload: Data can be uploaded as TEXT or CSV or Semicolon separated format. Please look into the example data file. A demo test dataset is running by default and it is available for download by clicking on the “List example data” button. UpSet module takes three types of inputs.

   i. List type data: List data is a correctly formatted csv/text file, with lists of names. Each column represents a set, and each row represents an element (names/gene/SNPs). Header names (first row) will be used as set names. ii. Binary type data: In the binary input file each column represents a set, and each row represents an element. If a names is in the set then it is represented as a 1, else it is represented as a 0. iii. Combination/expression type data: Combination/expression type data is the possible combinations of set intersections.

Parameters setup¶

2. Settings: there are multiple options to display the plot -

   i. select sets: select the dataset from the input data.

   ii. Number of intersections to show: Please add the number to calculate the intersection.

   iii. Order intersections by: From the drop-down menu, please select the intersection order -

   • Frequency
   • degree

   iv. Increasing/Decreasing: Please select the order of the frequency/degree.

   v. Scale intersections: Please select the scale intersection from the drop-down menu -

   • Original,
   • log10,
   • log2

   vi. scale sets: Please select the scale intersection from the drop-down menu -

   • Original,
   • log10,
   • log2

   vii. Plot width: select the plot width from the slider.

   viii. Plot height: select the plot height from the slider.

   ix. Bar matrix ratio: select the bar matrix ratio from the slider.

   x. Angle of number on the bar: slider to change the angle of the numbers on the bar.

   xi. Connecting point size: change the connecting point size .

   xii. Connecting line size: change the connecting line size.

3. Font & Color: multiple options are included for font and colours -

   i. Select color theme: Colour theme can be chosen from the drop-down menu.

   ii. Label font size: Change the font size of the Label.

   iii. Number font size: Change the font size of the number.

Result¶

User can download the figure in different format.

R packages used¶

1. UpSetR