Cluster files

Cluster files create the different ordinations plots of cells in the study. You are welcome to create as many of these plots as you would like. Each plot is created by loading a different file. These plots can be 2D or 3D and can contain metadata specific to just the plot (and not shared with other plots). These files/plots do not need to contain all your cells, giving you the freedom to plot subsets of your study for targeted visualization.

Format: This is a tab-delimited file with 3 required columns (with the option of more) and 2 required header rows.

Columns: Columns 1 - 3 are required and are as follows: cell name ("NAME"), X coordinate ("X"), and Y coordinate ("Y"). Additional columns can be included. If a fourth column Z coordinate ("Z") column is given, the plot will be 3D using the Z column as the third dimension. Any other additional columns included after the required columns ("NAME", "X", and "Y") will be treated as metadata to be potentially plotted on this plot but not other plots (global metadata should be in the metadata file). When defining cell names, please use alphanumeric characters; underscores are also valid. These cell names should match cell names in your other documents. Not all cells in the expression matrix must be in this file, you are welcome to plot subsets of your cell.

Rows: Rows are tab-delimited. The first two rows are required. The first row should start with "NAME", "X", "Y" and optionally "Z". Additional entries are the names of the optional plot-specific metadata you want to include in just this plot. These are the names the viewer will see when selecting metadata in the plot. The second row indicates what type of data is given in each column; "numeric" for continuous data or "group" for categorical labels. This row starts with "TYPE", "numeric", "numeric", and optionally "numeric" for the Z coordinate column. Additional entries will be either "numeric" or "group" indicating the data type of any additional columns. Starting at the third row, each row of this file is a point/cell in the plot with entries for each column (defining cell names, coordinates, and other associated metadata). Please note, cell names should match other cell names in other study files.

Example cluster file

Note: Required for study visualization.