Cluster Levels

The plot displays the relative expression of the selected gene(s) among clusters. The error bars represent binomially distributed sampling noise given the number of cells in each cluster; it does not represent heterogeneity in expression among cells within the cluster. Only clusters filtered in the Query panel are displayed. The plot is limited to only two entered genes. If more than two genes are chosen, then the display switches to a heatmap-like table.

Cluster Levels (Heatmap Table)

The table displays the relative expression of the selected gene(s) in all clusters using a shaded dot. Darker dots represent higher gene expression. Only clusters filtered in the ',b('Query'),'panel are displayed. Mouseover dots to display numeric values or choose the download icon to retrieve the full table data in R. The table is displayed when more than two genes are chosen.

Help for t-SNE plot of clusters in global region space.

Each point represents a single cell. Each cell is associated with a gene expression vector. This high-dimensional data is reduced using a set of automated independent components and projected onto two dimensions using t-SNE ('global space', i.e. representing all cells from a brain region/tissue). The cluster classifications are derived from Louvain clustering of the ICs.

Points are generally sub-sampled to improve display and speed rendering. Sampling can be controlled using the Display panel on the left. 'Bag' plots show the distribution of all points similar to a one-dimensional box plot. The darker region represents 50% of cells. The lighter region represents all points except outliers.

Clusters are highlighted in different colors based on the filtering choices in the Query section in the left panel. Labels and other display features can be customized in the Display panel

If a row in the differentially expressed genes table, below, or one or more genes are entered by name in the Query panel to the left, then the selected genes' expression levels will be displayed in black (one row of t-SNE plots per gene) and the mean expression level for that gene in the subcluster is displayed by a color gradient or transparency, depending on settings.

Cluster scatter plot

Each point is the mean log normalized transcript count among all cells in the target and comparison clusters (or region). Large points meet the fold ratio and transcript amount criteria in the Clusters panel. Points are shaded according to their significance. Selected rows in the table of differentially expressed genes are displayed in green or red depending on whether they pass the criteria.

Filtered Table of Clusters

The table displays all matching clusters based on the filtering parameters set in the ',b('Query') panel on the left. Other plots and display outputs are limited to the clusters listed here.

Differentially expressed genes in clusters

Select a 'target' cluster in the left Clusters panel to display those genes that are over-expressed in that cluster with respect to the remaining cells in the region or a chosen comparison cluster. Adjust filter criteria using the Clusters panel.

Any manually added genes are always displayed in the table and colored green if the expression criteria is met and colored red otherwise.

One or more rows can be selected to display gene expression in the t-SNE and scatter plots.

Subcluster Levels

The plot displays the relative expression of the selected gene(s) among subclusters. The error bars represent binomially distributed sampling noise given the number of cells in each subcluster; it does not represent heterogeneity in expression among cells within the subcluster. Only subclusters filtered in the Query panel are displayed. The plot is limited to only two entered genes. If more than two genes are chosen, then the display switches to a heatmap-like table.

Subluster Levels (Heatmap Table)

The table displays the relative expression of the selected gene(s) in all subclusters using a shaded dot. Darker dots represent higher gene expression. Only subclusters filtered in the Query panel are displayed. Mouseover dots to display numeric values or choose the download icon to retrieve the full table data in R. The table is displayed when more than two genes are chosen.

Help for t-SNE plot of subclusters in global region space.

This plot is like the t-SNE plot of clusters in global region space, but displays the subcluster labels for each cell.

Help for t-SNE plot of subclusters in local cluster space.

Each point represents a single cell. Each cell is associated with a gene expression vector. This high-dimensional data within a cluster is reduced using a set of curated independent components and projected onto two dimensions using t-SNE ('local cluster space'). The subcluster classifications are derived from Louvain clustering using a subset of the ICs.

Subcluster regions are highlighted in different colors based on the filtering choices in the Query section in the left panel. All points in the corresponding cluster are displayed with points outside of the chosen subcluster(s) shown in gray and all points in the chosen subclusters displayed in color. (There is no subsampling for subcluster displays.)

If a row in the differentially expressed genes table, below, or one or more genes are entered by name in the Query panel to the left, then the selected genes' expression levels will be displayed in black (one row of t-SNE plots per gene) and the mean expression level for that gene in the subcluster is displayed by a color gradient or transparency, depending on settings.

Labels and other display features can be customized in the Display panel

Subcluster scatter plot

Each point is the mean log normalized transcript count among all cells in the target and comparison subclusters (or region). Large points meet the fold ratio and transcript amount criteria in the Clusters panel. Points are shaded according to their significance. Selected rows in the table of differentially expressed genes are displayed in green or red depending on whether they pass the criteria.

Filtered Table of Subclusters

The table displays all matching subclusters based on the filtering parameters set in the ',b('Query') panel on the left. Other plots and display outputs are limited to the subclusters listed here.

Differentially expressed genes in subclusters

Select a 'target' subcluster in the left Clusters panel to display those genes that are over-expressed in that subcluster with respect to the remaining cells in the region or a chosen comparison subcluster. Adjust filter criteria using the Clusters panel.

Any manually added genes are always displayed in the table and colored green if the expression criteria is met and colored red otherwise.

One or more rows can be selected to display gene expression in the t-SNE and scatter plots, above.