Hi @coralgal! We don't currently support importing CSV or TSV formatted OTU tables. We have an open issue tracking this feature, and we'll follow up here when it's available in a release!
In the meantime, you can use the biom convert tool (which comes installed with QIIME 2) to convert your CSV OTU table into a .biom file. See the biom convert tutorial for details; you'll first need to convert your CSV file to TSV. Both JSON and HDF5 versions of the .biom file format are supported by the QIIME 2 importer. Once you have a .biom file, follow this section of the importing guide to import your .biom file into a FeatureTable[Frequency] artifact (or FeatureTable[RelativeFrequency] if your data are relative abundances instead of counts).
Once you have a feature table artifact, you can use diversity core-metrics-phylogenetic or diversity beta-phylogenetic to perform weighted UniFrac analyes. See the Moving Pictures tutorial for examples of alpha and beta diversity analyses. To produce heatmaps of your feature table, check out feature-table heatmap.
The imported .biom file will be a FeatureTable[Frequency] artifact. If you have a phylogenetic tree, where tree tips correspond to features in the feature table (e.g. OTUs), you can import a Newick file following this section of the importing guide. Only an example of importing an unrooted tree is shown, but if you have a rooted tree the process is largely the same, you'd just use --type Phylogeny[Rooted]. Once you have a rooted phylogeny, you can use the tree in phylogenetic diversity analyses such as weighted UniFrac (the Moving Pictures tutorial describes the tree building and rooting steps).
If you're new to QIIME 2 or these types of analyses, I recommend checking out the Getting Started guide. The tutorials are a great way to not only learn QIIME 2, but also to discover different techniques for analyzing and visualizing the data you have on hand. Let us know if you have follow-up questions (preferably in separate forum topics).