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To use the Merge cells option, the data matrices (one or more) that are to be merged with the currently selected one should have the same features (e.g. genes), but distinct cells. Push the Select data nodes button and Partek Flow will display you a preview of the pipeline; the data nodes that can be merged are shown in blue. Click on the data node that you want to merge with the current one and push the Select button. The selected node will be shown under the Select data nodes button (Figure 2). Repeat the procedure if you would like to merge additional nodes. If you made a mistake, use the Clear selection icon. Push Finish to proceed.

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To use the Merge features option, the data matrices (one or more) that are to be merged with the currently selected one should have the same cells features, but distinct features (e.g. gene and protein expression). Push the Select data nodes button and Partek Flow will display you a preview of the pipeline; the data nodes that can be merged are shown in blue. Click on the data node that you want to merge with the current one and push the Select button. The selected node will be shown under the Select data nodes button. Repeat the procedure if you would like to merge additional nodes. If you made a mistake, use the Clear selection icon. Push Finish to proceed.

Task Output

The output of the Merge matrices task is a Merged counts data node (Figure 3). 

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Depending on your goal, you may want to consider a different approach. For example, data matrices based on two different assays (e.g. gene and protein expression) can be combined using Find multimodal neighbors. Instead of merging two (or more) cell populations by using Merge cells, you may want to use filtering (Filtering > Filter groups) to filter out the populations that you do not consider relevant / filter in the populations of your interest.

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