Sample Group Overview and Tumor Microenvironment
The development team has been hard at work adding new modules to the portal. Some of the features include: the group overlap where you can see how different subtype definitions overlap, visualized in a mosaic plot. An example here is the TCGA molecular subtypes vs the immune subtypes.
Then, in the Tumor Microenvironment module, bar plots show the breakdown of stromal vs immune cell content within each immune subtype. Clicking on a bar shows the underlying data, lymphocyte vs stromal fractions, as a dot plot. Below that, the cell type content of each subtype is shown. You can select different fraction types which take your view from different levels of granularity. At the finest grain, we have the most distinct cell types. Moving to coarser grained views, cell types are summed up. For example, the various states of macrophage, ‘M0 M1 M2’, are summed into a single ‘Macrophage’ quantity.