Visualization

How do I order my heatmap by the cell types?

If you would like specific groups (e.g. cell types) in a certain order, do not perform Hierarchical clustering on these cells and instead choose to assign order, then use click and drag to reorder the groups. If you want to remove a group, you can choose to exclude this group in the filtering section. You can still perform Hierarchical clustering on the features if you would like to. Hierarchical clustering will force the heatmap to cluster and you would need to click the dendrogram nodes to switch the order. Click here for more information.

How do I display UMAP for each sample in the Data Viewer?

For a multi-sample project, all of the downstream tasks will be run separately if 'Split by sample' was checked when performing the PCA task. Visualization of different samples can be displayed by 'Sample' using the 'Misc' section in the Axes card. To show different samples side by side, one can click 'Duplicate plot' first, then use the 'Sample' option to switch the samples.

Can I visualize fold change values on a heatmap without using a z-score?

Yes, the default settings can be modified by clicking "Configure" in the Advanced settings during task set-up, then change the "feature scaling" option to "none" to plot the values without scaling. For more information related to the heatmap click here.

Why don't I see Flip mode on the heatmap? Why can't I download all of the data after zooming?

The Flip mode and download all data options are disabled if there are more than 2.5 million values (rows x columns) in the heatmap.

How to label gene names on volcano plot?

By default, genes are selected if the p-value is <=0.05 and |fold change| >=2 and when the number of selected genes is less than 2000 genes, they will be labeled. You can click on Style button in Configure section, choose a gene annotation field from the Label by drop-down list to change the label. If you number of selected genes is select less than or equal to 100, Partek Flow will try to spread out labels as much as possible to clearly display the labels. If number of selected genes is more than 100, labels will be next to the selected genes, there will be overlaps where genes are close together. If there are more than 2000 genes selected, no label will be displayed.

If you click any blank space, you can turn off select and use different selection mode button on the vertical bar on the upper-right corner of the plot to manually select dots on the plot.