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Welcome to the UpSetR Shiny App!


UpSetR generates staticUpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.


To begin, input your data using one of the three input styles.

  1. "File" takes a correctly formatted.csv file.
  2. "List" takes up to 6 different lists that contain unique elements, similar to that used in the web applications BioVenn (Hulsen et al., 2008) and jvenn (Bardou et al., 2014)
  3. "Expression" takes the input used by the venneuler R package (Wilkinson, 2015)

To view and explore your data click on the "Plot!" button.


For further details about the original technique see theUpSet website. You can also check out the UpSetR R package and its source code.

If you use UpSetR in a paper, please cite:

Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983–1992, 2014. doi:10.1109/TVCG.2014.2346248

Instructions

To use this method, begin by uploading a correctly formatted .csv file. A correctly formatted .csv file is encoded in binary and set up so that each column represents a set, and each row represents an element. If an element is in the set it is represented as a 1 in that position. If an element is not in the set it is represented as a 0.


After uploading the file, choose the correct separator. If the elements in each column are seperated by a ' , ' choose comma, by a ' ; ' choose semicolon, or by tabs choose tab.


To see what a correctly formatted data set with a comma (' , ') seperator looks like download the movies file below.

Download the movies data set here!


Instructions

The input style of lists is useful when wanting to compare sets by supplying , say a list of gene IDs or SNPs. To use this format enter a list of elements seperated by a comma to each input box. These elements can be entered as numbers, letters, IDs, words, etc. The only limitation to entering the lists is having spaces in the element names. As an alternative an underscore (' _ ') character can be used to to substitute for the spaces. To give each set a name, enter the names into the bars where the word 'List' followed by a number is grayed out.



To see how the list format works copy and paste each list of letters into their respective input boxes.


List 1: A, B, C, D, E, F, G, H

List 2: A, B, D, F, I, J, K, L

List 3: A, H, J, M, N, O, P, Q

List 4: B, L, O, P, R, S, T, U


Instructions

The expression input style allows the user to name each intersection and assign a size to it. When including an intersection of degree 2 or more, the names of the sets that make up the intersections are seperated by an ampersand (' & '). The names of the sets can be any string. The only limitations of the set names is that they cant contain any spaces. As an alternative an underscore (' _ ') character can be used to to substitute for the spaces.



Here is an example of an expression input. Copy and paste it into the input box to see how it works.


A=12, B=12, C=5, A&B=4, A&C=2, B&C=1, A&B&C=2

expression input


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