Select one KEGG or Reactome pathway or GO biological process.

There are four options to filter the number of rows shown:

If you select this option, you can choose one dataset at a time. On the right, the numeric matrix contains only integers and the last annotation row cannot be detected automatically. On the left, the numeric matrix contains non-integer values and the last annotation row is detected correctly. The situation is depicted on the following images where there are three annotation lines and the green and red line show automatic detection. some grade coded with integers: 1, 2, 3). fractional numbers) and there are some left columns or top rows that contain integers only, these first rows and/or columns are considered integer-valued annotations (e.g. If the matrix contains non-integers (i.e. When finding number of annotation rows and columns, the largest possible numeric matrix from bottom right corner is found. We use the heuristic where minimum is taken over all rows and the delimiter with the greatest score is chosen as the right one. To find delimiter, it counts for each possible delimiter (comma, tabulator, semicolon) how many times it appears on each row.

If automatic detection of the column and row annotations is not working correctly, try to set it manually (uncheck the 'detect column and row annotations' checkbox).įor user-uploaded datasets, ClustVis automatically detects both delimiter and number of annotation rows from the data by default.

If automatic detection of the delimiter is not working correctly, try to set it manually (uncheck the 'detect delimiter' checkbox).

Make sure all missing values are marked with NA or empty cell.

Make sure there are no duplicate row or column names.

In case of doubt, it is safer to open the data in a spreadsheet program and copy-paste from there rather than choosing a file for upload. Make sure all rows have equal number of columns.Make sure file is chosen for upload or pasted to the text box.

If your dataset is not uploaded correctly (no rows are shown), please check the following: It is also possible to use one of the testing datasets to get an overview of the web tool. The latter case is described more closely in the next section. Which has a collection of public datasets from In addition, it is possible to load settings that you have saved earlier (including data, drop-down settings etc.) or import data from Uploading Excel native files directly (.xls or. tab) and then upload this file to ClustVis. MS Excel), you can copy-paste the data to 'Paste data' box or export the data as delimited text file (ending with. When taking data from spreadsheet program (e.g. Annotations are optional, data sets without annotations can be uploaded as well (on the example image, omitting rows 2-4 and/or columns B and C). Format of the input file is shown on the image below. Annotation labels are in the first row and column, respectively.

Row labels and annotations are left from the matrix, column labels and annotations are above the matrix. The numeric data matrix is situated in the bottom right corner, dimensions presented in rows and points in columns. Though, when version of ClustVis changes, old saved settings may not be fully compatible with the new version if e.g. There is no planned expiration time for the links, users can delete the settings if they are concerned about the privacy. This can also be used to send a link to a collaborator to show the same view. To save uploaded data and selected settings, you can use a button on the 'Export' tab, a link is given to recover the settings later. The idle timeout (the time when browser session ends if user is inactive) is set to 30 minutes from server side but this can be overridden by browser configuration.

Export - create link with current settings, download intermediate results.

Data pre-processing - option to aggregate columns with similar annotations, remove rows/columns with missing values, row centering and scaling, method for calculating principal components and imputing missing values.

Data import - choose input dataset, option to filter rows/colums based on annotations and transpose matrix.

In general, different tabs provide the following options: When moving from one tab to another, settings are saved automatically. All tabs work in a similar way: you can choose settings from the left panel, image or table on the right will automatically renew after that. You can move through the analysis steps by going to each of the tabs from left to right.

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