Comments (3)
sreichl
commented on June 12, 2024
make a separate plotting function
- Gets wrapped plot panel or list of plots?
- Gets Output path with _1
- Gets calculated output dimensions of the base plot (ie one) and legend
- Gets number of rows and cols and number of plots
- Based on input decide how many plots and dimensions
- Make folder per plot type eg violin_plots
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sreichl
commented on June 12, 2024
If there are too many then plot them individually
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sreichl
commented on June 12, 2024
Use output directory as result of the rule and use nested directories to encode metadata in addition to the file name.
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Related Issues (20)
- save result object in h5ad format for better interoperability with other packages HOT 2
- Cyclic graph dependency when metadata not provided
- extend KOcall strategy beyond singlets HOT 1
- dynamic memory for data intense rules depending on input
- make normalization configurable
- order all plot panels alphabetical
- speed up rule save_counts (bottleneck) HOT 1
- add example data
- extend pseudobulking functionality
- update documentation
- add support for additional metadata file emerged from downstream analyses HOT 1
- full tests on new functions
- add support for generic gene by barcode/cell count matrices
- all heatmaps should be hierarchically clustered eg using hclust
- update to sctransform to use vst.flavor="v2"
- make dot plot color scale centered at 0
- pseudobulking of counts by metadata feature
- background noise removal using CellBender HOT 1
- generalize to other modalities e.g., sc/snATAC-seq
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