# `plyxp` `plyxp` provides efficient abstractions to *SummarizedExperiment* such that using common dplyr functions feels as natural to operating on a *data.frame* or *tibble*. `plyxp` makes use of a concise grammar for exploring and manipulating annotated matrix data in the form of the *SummarizedExperiment*, scaling from simple to complex operations spanning one or more tables of data. We also aim for optimized implementations in `plyxp` to power some functionality within the `tidySummarizedExperiment` package, which also offers a dplyr-like interface to *SummarizedExperiment*. These two packages can easily be used in parallel, by casting objects with the `new_plyxp` constructor to enable `plxyp`-driven functionality. `plyxp` uses [data-masking](https://rlang.r-lib.org/reference/topic-data-mask-programming.html) from the `rlang` package in order to connect dplyr functions to *SummarizedExperiment* slots in a manner that aims to be intuitive and avoiding ambiguity in outcomes. ***Note:*** This package is still under active development. Feel free to reach out to the package developers, see *Feedback* section below. ## installing `plyxp` ```r # plyxp is available on BiocManager version 3.20 BiocManager::install("plyxp") ``` # data masking `SummarizedExperiment` \ The `SummarizedExperiment` object contains three main components/"contexts" that we mask, the `assays()`, `rowData()`[^1] and `colData()`. [^1]: At this moment `rowRanges()` is not supported in `plyxp` but may become its own pronoun in the future. ](man/figures/Overview-bindings.png) \ `plyxp` provides variables as-is to data **within their current contexts** enabling you to call S4 methods on S4 objects with `dplyr` verbs. If you require access to variables _outside the context_, you may use pronouns made available through `plyxp` to specify where to find those variables. ](man/figures/Overview-pronouns.png) \ The `.assays`, `.rows` and `.cols` pronouns outputs depends on the evaluating context. Users should expect that the underlying data returned from `.rows` or `.cols` pronouns in the _**assays context**_ is a vector, replicated to match size of the assay context. \ Alternatively, using a pronoun in either the `rows()` or `cols()` contexts will likely return a list equal in length to either `nrows(rowData())` or `nrows(colData())` respectively. # Feedback We would love to hear your feedback. Please post to [Bioconductor support site](https://support.bioconductor.org) or the `#tidiness_in_bioc` Slack channel on community-bioc for software usage help, or post an [Issue on GitHub](https://github.com/jtlandis/plyxp/issues), for software development questions. # Funding `plyxp` was supported by a EOSS cycle 6 grant from The Wellcome Trust.