todo.org

AcidPlots

Development

matchLabels: Rework support for default NULL or empty list here.

Rework heatmap engine to use ComplexHeatmap instead of pheatmap.

Check that plotQC SCE method returns interestingGroups in plot legend correctly.

Need to think about NA gene symbol handling in call to convertGenesToSymbols.

Harden plotCounts to error faster on gene identifier mismatch.

Consider adding assay support to plotCountsPerCell.

May want to harden plotCounts against DESeqDataSet input.

We don’t want to ever plot non-normalized counts by default.

How to suppress joint bandwidth message for ridgeline?

Consider making the theme_acid_plots less bold by default.

Create a plot for log2 vs. log2 expression of RNA-seq counts.

Improve passthrough argument documentation for `plotCorrelationHeatmap`

and other heatmap functions that inherit from `plotHeatmap`.

Need to add improved support for X-Y scatterplot with correlation

information on the plot.

colors: colorscope, dracula, craylola

GSEA heatmap code (put this in pfgsea).

plotHeatmap needs include basic matrix method.

Add venn diagram support? See ggVennDiagram.

Kind of like upset plots more.

Consider adding matrix support for plotHeatmap.

Note that this won’t include interesting groups.

Add support for multiple PCs in `plotPCA()`.

Currently `plotPCA()` functions simply to plot PC1 vs. PC2. It is useful to visualize the other components in a series (e.g. PC3 vs. PC4 in addition), which isn’t currently supported in the function. We may want to add an option to display a plot grid of PC1 through PC10.

Consider switching heatmap engine.

Switch pheatmap to ComplexHeatmap or heatmap.2?

`plotHeatmap()`: Look into kmeans approach with `kmeans_k`.

Is plotCountsCorrelation not matching geneID to geneName?