has2k1/plotnine: v0.8.0

Kibirige, Hassan; Lamp, Greg; Katins, Jan; gdowding,; Austin, '; matthias-k,; Funnell, Tyler; Finkernagel, Florian; Arnfred, Jonas; Blanchard, Dan; Astanin, Sergey; Chiang, Eric P.; Kishimoto, Paul Natsuo; Sheehan, Evan; stonebig,; Willers, Bernard; Gibboni, Robert; smutch,; Halchenko, Yaroslav; Pavel,; King, Brian; Rk, Min; Collins, John J.; zachcp,; ANTHONY, Anthony; Koopman, Bevan; Grohmann, Carlos Henrique; Becker, D.; Brown, Dan; Saiz, Daniel

doi:10.5281/zenodo.4636791

Cited by 8 publications

(5 citation statements)

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“…Output data from the described tools were processed using Python version 3.8.3 [74] and R version 4.1.0 [68]. Figures were generated using plotnine in Python [75] or ggplot2 [76] in R with organization into panels using patchwork 1.1.2 [77]. Statistical analysis on the data was performed with SciPy [67] or with R version 4.1.0 [68].…”

Section: Data Processing and Visualizationmentioning

confidence: 99%

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

et al. 2023

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Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

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Section: Data Processing and Visualizationmentioning

confidence: 99%

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

et al. 2023

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“…Representative visualizations of the energetic minima for each system are in Figure . The visualizations were made using the plotnine package for Python …”

Section: Methodsmentioning

confidence: 99%

Effect of Graft Length and Matrix Molecular Weight on String Assembly of Aligned Nanoplates in a Lamellar Diblock Copolymer

et al. 2022

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Grafted nanoparticle polymer composites have been used to create a highly bespoke class of materials, with spherical nanoparticles serving as the gateway design into this class. Grafted nanoplates (nanoparticles where the radius is longer than the height of the particle) provide opportunities and pathways to control overall system properties through their anisotropic properties. Current research on addressing the challenges associated with assembly is quite limited and unexplored. Using hybrid particle/self-consistent field theory (hSCFT) simulations, we build upon our previous work examining polyethylene glycol (PEG) grafted nanoplates within a nearly symmetric (f ≈ 0.5) lamellar poly(styrene-b-methyl methacrylate) (PS-b-PMMA) block copolymer (BCP) matrix. We examine the interplay between the nanoplate graft length and matrix molecular weight and their effect on the potential of mean force (PMF). Ultimately, we discover that the location and depth of both the energetic well (local minimum) and the energetic barrier (local maxima) of the PMF, as well as the existence of the local maxima, are dependent on the relative width of the nanoplates to the lamellar domain, with the longer grafts experiencing deeper energetic wells and further interplate separation distances. The results are driven by the interfacial tension due to the local domain bulging effects caused by the insertion of the nanoplates into the lamellar system. With experimental separation distances of a PEG-grafted gadolinium trifluoride doped with ytterbium and erbium, GdF3:Yb/Er (20/2 mol %) nanoplates corroborate the correlation found in the simulations between larger matrix domains and a widening of the energetic well. Additionally, the average separation distance follows a trend similar to the hSCFT data. We anticipate these results to help in the development and design of anisotropic nanoparticles within BCPs to create nanocomposites tailored for specific applications and properties.

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“…Output data from the described tools were processed using Python version 3.8.3 ( Van Rossum and Drake Jr, 1995 ) and R version 4.1.0 ( R Core Team, 2021 ). Figures were generated using in Python Kibirige et al (2021) or ( Wickham, 2016 ) in R with organization into panels using ( Pedersen, 2020 ). Statistical analysis on the data was performed with ( Virtanen et al, 2020 ) or with R version 4.1.0 ( R Core Team, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

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et al. 2022

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Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of communities of multiple species. Metatranscriptomics in particular offers an understanding of real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. However, these approaches are rarely validated. A systematic validation of metatranscriptome assembly and annotation methods is necessary to appropriately assess (1) the fidelity of our community composition measurements and (2) the confidence of novel taxonomic and functional content discovered with metatranscriptomics. Here, we present eukrhythmic, an automated and customizable multi-assembler workflow for eukaryotic metatranscriptome assembly, annotation, and analysis, and validate the ability of the pipeline to recapitulate simulated eukaryotic community-level expression data treated as a gold standard. Finally, we apply this pipeline to two previously published metatranscriptomic datasets, showing both recapitulation of previous results as well as enhanced taxonomic and functional gene discovery.

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has2k1/plotnine: v0.8.0

Cited by 8 publications

References 0 publications

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

Effect of Graft Length and Matrix Molecular Weight on String Assembly of Aligned Nanoplates in a Lamellar Diblock Copolymer

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly

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