Create Heat Map for Cell Abundance

Create Heat Map for Cell Abundance compares two groupings of the same cells. It outputs a heat map showing the cell abundance for the two groupings. The tool is useful for matching automated clusters with predicted cell types or for comparing analysis that has been run in third party tools with the results obtained using the CLC Single Cell Analysis Module.

The tool produces a Heat Map (Image heatmap_16_n_p) of cell abundance. It is often most natural to run the tool from a Dimensionality Reduction Plot by right-clicking on the plot, see UMAP and tSNE plot functionality for details. However, it can also be found in the Toolbox here:

        Cell Annotation (Image sc_cell_annotation_folder_open_16_n_p) | Create Heat Map for Cell Abundance (Image cell_abundance_heatmap_16_n_p)

The tool requires at least one Cell Clusters (Image cell_clusters_16_n_p) and/or Cell Annotations (Image cell_annotations_16_n_p). A number of options are available to choose and order the groups:

While numerical categories can be selected from Cell Annotations, it is often most relevant to choose discrete traits.

Each colored rectangle in the heat map represents the number of cells found in both groups. Three options exist for scaling the numbers:

When selecting "By all", the most abundant pairs of groups will be most noticeable, whereas "Per row / column" highlights how well different groupings match and shows the composition of one of the groupings as a function of the other.



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