This tool generates an overview of flow data clustering analysis results.

Tip: Marker names need to be in the Cell Ontology for flowCL to run. .. class:: warningmark The number of populations or clusters this tool can handle is limited to 40. Output The output is a page with multiple tabs that allows visualization of the data. .. class: warningmark The input table is proportionally downsampled to 20K events for the visualization. .. class:: warningmark The output of this tool is interactive. However, comments or any other modifications made are not saved when exiting the view. ----- Example Input - fluorescence intensities per marker and population ID per event:

Marker1 Marker2 Marker3 ... Population
33      47      11      ... 1
31      64      11      ... 6
21      62      99      ... 2
14      34      60      ... 7
...     ...     ...     ... ...

Output Summary of the data: The comment field of this table is editable, and can be used to name the populations. The edited values are used to populate the legends of the other graphs. The columns are re-orderable. The 'col visibility' button allows to choose which columns to display. 'CSV', 'PDF' and 'Copy' respectively allow to download a comma-separated values file, a pdf version or to copy to your clipboard in a tab-separated format the current view of the table. .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Fsummary.png .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Fedit_summary.png Scatterplots overview: .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Foverview.png 2D Scatterplot: The user can choose which populations and markers to display. The Plotly toolbar allows more control over the display of the graph. There is an option to save the plot as a png file. .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Fscatter2D.png 3D Scatterplot: The user can choose which populations and markers to display. The Plotly toolbar allows more control over the display of the graph. There is an option to save the plot as a png file. .. class:: warningmark Unfortunately Chrome stopped supporting the plugin enabling this visualization. If you get an error message stating that WebGL is not supported, try switching to Firefox. .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Fscatter3D.png Parallel Coordinates: The user can reorder the markers, and choose which populations to display either by selecting them in the legends via checkboxes or by selecting them on the graph. Data selected for display is shown in the table below the graph. Mousing over a line in that table highlights the corresponding line on the graph. The 'col visibility' button allows to choose which columns to display. 'CSV', 'PDF' and 'Copy' respectively allow to download a comma-separated values file, a pdf version or to copy to your clipboard in a tab-separated format the current view of the table. .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Fpcflock.png Summary Statistics Boxplots: The user can choose whether to group the boxplots per marker or per population. By default, the values displayed are the 25th, median and 75th percentiles. The whiskers represent 1.5 times the interquartile range. The MFI or the values can be displayed by checking the corresponding checkboxes. The number of markers that can be plotted simultaneously is limited to 5. The number of outliers per data point is limited to 100. If there are more than 100 outliers, they are downsampled randomly to a 100 and a warning message is displayed. .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2Fbpflock.png If the ontology option was selected, the following tab is displayed. The CL terms hyperlink to their representation in the Immport Cell Ontology browser. The full flowCL run summary is accessible by clicking on the phenotype. .. image:: /repository/static/images/b98f8819313e7e18/..%2F..%2Fstatic%2Fimages%2Fflowtools%2FprofileCL_go.png