Tools for adjusting UMAPs

By default, the UMAP is the main centre plot you see once you run and view an analysis. Here are some of the details on visualisation tools for the UMAP and the customisation you can do for the plot, cluster labels, colour palettes, etc.

Cell details on UMAP

You can hover your mouse over a data point on the UMAP for details on the cell, such as the cluster or group it belongs.

Directly below the plot area, the bar will show the total number of cells used for your analysis and on your UMAP. This number might be different from the initial number of cells you had in your dataset if you have filtered out cells in your analysis.

When you hide cells from the UMAP, this number will show the number of cells currently visible out of the total number of cells analysed.

When you select cells, the number behind the lasso icon is the number of cells selected, followed by the names of the clusters these cells belong to.

Annotation mode

Annotation mode is a shortcut to highlight and view cluster names, and edit cluster properties by directly interacting with the cluster of cells on the UMAP. You can exit annotation mode by clicking on the icon again.

_{💡Tip:  Use annotation mode to label clusters on your UMAP for snapshots}

Pan and Zoom

This allows you to click and drag the UMAP to move around the plot area. You can use scroll to zoom in or out of the plot.

Zoom to selection

When you have selected a cluster or clusters, you can quickly zoom into the selection.

_{💡Tip: Combine tool functions! You can activate annotation mode for cluster labels, select and zoom into a cluster of interest and create a new snapshot}

Reset zoom

This will reset the zoom on the UMAP to its default position.

Take snapshot

This will capture the current view of the UMAP and save it on the platform.

Snapshots

Here you will find all the captured snapshots and tools to edit the name, download and delete your snapshots. The cluster name and the number of cells in each cluster are also added to every image.

Switch plots

You can switch the default UMAP on the main plaot for t-SNE or any coordinates for a plot you have imported for this dataset.

Scatterplot settings

In scatterplot settings, you have the options to customise the points on the plot, add axis labels and change the colour palette of the plot.

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Adjusting colour saturation of features

When visualising the gene or feature on the UMAP, outliers in the expression values can skew the colour saturation on the UMAP. This can be resolved by adjusting the colour saturation slider from Scatterplot settings to exclude the outliers and increase the visibility of the gene expression in relevant cells on the UMAP.

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UMAP Clusters

On the left of the UMAP, we have the tools and options for clusters, imported cell annotations and cluster markers.

The Group by dropdown contains all cluster information from the analysis run and groups for imported cell annotations can be found here as well.

Change clusters shown on UMAP

Leiden clusters are shown on the UMAP by default. You can change to a different cluster resolution or view cells in groups from imported cell annotations from the Group by dropdown menu.

Edit cluster properties

Here you can rename the cluster, change the colour of the clusters and hide a cluster of cells from the UMAP. You can also click and drag to reorder the list of clusters or groups. You can also rename all the clusters by importing a comma-separated table (csv) file with the current cluster names and their new cluster names.

Hide cells on UMAP

You can hide clusters or groups of cells on the UMAP. Note that hidden cells are not actually removed from the analysis, they are only excluded visually on the UMAP and when selecting cells.

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