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Expand functionality of plotGene and add new utility functions #108

Merged
merged 11 commits into from
Aug 26, 2019
Merged

Expand functionality of plotGene and add new utility functions #108

merged 11 commits into from
Aug 26, 2019

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vkozareva
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Allow plotGene to plot:

  • Values scaled by different groupings based on features in cell.data (in addition to raw, norm values)
  • Plots organized by different groupings in cell.data (instead of just by dataset)
  • With min and max clips

Also added more color options to both plotGene and plotFeature.

New functions:

  • reorganizeLiger (set up new liger object with datasets split by other feature in cell.data)
  • getProportionMito

@vkozareva
Add more color options to plotFeature
d8eb9a1
@vkozareva
Add function to calculate proportion mitochondrial contribution
f9068e6
@vkozareva
Revamp plotGene function
a018600 
Add option to scale by different groupings of cells.
Add option to plot by different groupings of cells.
Add new color options. Add option for min and max cutoffs.
@vkozareva
Add reorganizeLiger function
eddd884
@vkozareva
Add more color options to plotFeature
cd15f6b
@vkozareva
Add function to calculate proportion mitochondrial contribution
eb23c50
@vkozareva
Revamp plotGene function
769f62a 
Add option to scale by different groupings of cells.
Add option to plot by different groupings of cells.
Add new color options. Add option for min and max cutoffs.
@vkozareva
Add reorganizeLiger function
98d6487
@vkozareva
Update walkthrough pdf
906a375
@vkozareva
Add tests for plotGene, reorg function, and getProportionMito
ac247fa 
Also minor documentation changes.
@vkozareva
Merge branch 'split-plotting' of https://github.com/MacoskoLab/liger …
e4c4504 
…into split-plotting
@vkozareva vkozareva merged commit 622f23a into master Aug 26, 2019
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@vkozareva