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Added vdiffr into testing, nessecary files for Rcpp, seurat command, and minor syntax changes #256

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merged 11 commits into from
Aug 11, 2023

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@Qile0317 Qile0317 commented Aug 8, 2023

As scRepertoire has lots of plotting functions, I begun some testfiles for testing of plot outputs with the vdiffr package. Also added the src folder and some dummy files for future Rcpp functions. Also copied over the code for adding seurat commands to seurat objects after calling combineExpression. (I think it's a good practice to add the seurat object's @command attribute when the object is modified)

Couldn't figure out how to fix the annoying R CMD check warning but there's probably some easy fix I'm missing with the dependencies, or the data file for screp_example might need to be updated?

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Qile0317 commented Aug 9, 2023

Also 2 minor additions; modified quantContig so that it displays results for single sample runs slightly better, without the NA label; and added an optional argument seed into scatterClonotype at the end, so that geom_jitter could produce deterministic plots for slightly better reproducibility and testing purposes

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Also added a new exported data file called combined_mini_contig_list which is a subset of contig_list that also had combineTCR ran on it. The subset only has rows corresponding to the barcodes in screp_example. Its quite useful for testing but its up to you whether you think it should be exported or remain as internal data

@ncborcherding ncborcherding merged commit 260f4e4 into ncborcherding:qile Aug 11, 2023
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