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DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R
https://davislaboratory.github.io/standR/
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QC plotting functions #1

Closed bhuvad closed 2 years ago

bhuvad commented 2 years ago

I have added implementations to plot PCA, MDS, RLE, and other reduced dimension plots. These implementations work for ExpressionSet, DGEList, SummarizedExperiment, SingleCellExperiment, SpatialExperiment and ExperimentList objects. The following user interface functions are added:

  1. plotPCA()
  2. plotMDS()
  3. plotDR()
  4. plotRLE()

I have also added a plotting theme function bhuvad_theme() and a package checking function (checkPackages()) for internal use. The latter will be useful when checking dependencies for optional functions.