This view displays cell-type score data derived from RNA-Seq expression for a given method/cell type with respect to chosen sample attributes. Cell types are currently derived from two methods:

MalCT_PCA—This is the PC1 score computed from the van Galen et al 2019 malignant cell type gene sets where bone marrow derived samples were centered and scaled separately from peripheral blood.

xCell—Scores as derived using the xCell method with bone marrow derived samples scored separately from peripheral blood.

Mutations (rolled up to genes) can be compared between highest and lowest expression samples for the given gene.

Global filters affect this view. Any sample-based filters set here and/or variant filters set here determine what samples and variants appear in this view.

A small gray summary plot showing scores for all samples for the selected cell type appears at top left.

In the large plot to the right, the same cell-type data is plotted relative to the selected sample attribute, with a dotted median line for each group if the selected attribute is categorical.

In the "Compare groups" section, groups of genes are shown as color-coded segments of a circle. The three segments represent genes carrying mutations only in the highest-scoring samples, those with mutations only in the lowest-scoring samples, and those with mutations in both groups.

Select a Method and Cell type via the drop-down menus at top left to view corresponding scores.

Select a sample attribute from the drop-down menu at top middle to stratify samples accordingly.

For long sample attribute labels that have been truncated, mousing over them will reveal the full text of the label.

Below the large plot, to compare highest and lowest-expression samples, adjust the percentage (if desired), and click "Submit."

Data can be exported via the green arrow buttons and plots generated using the PDF and PNG buttons.