Violin SuperPlots: visualizing replicate heterogeneity in large data sets

Kenny, Martin; Schoen, Ingmar

doi:10.1091/mbc.e21-03-0130

Cited by 33 publications

(33 citation statements)

References 12 publications

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“…Distributions of capsid and virion widths were illustrated using a Violin SuperPlot [ 102 ], with data grouped by source tomograms. The stacked area plots for the proportion of infected cells at different stages of infection were generated using the ggplot2 package [ 103 ] in R studio [ 104 ].…”

Section: Methodsmentioning

confidence: 99%

“…The distribution of vesicle widths were illustrated using a SuperPlot [ 105 ], with data grouped by source tomograms. The numbers of mitochondrial branch points (branching nodes) were illustrated using a Violin SuperPlot [ 102 ], with data grouped by replicate. A two-tailed paired t-test was used to compare the width of the nuclear envelope at a site of primary envelopment with the width of the nuclear envelope elsewhere on the same tomogram using Excel (Microsoft).…”

Section: Methodsmentioning

confidence: 99%

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Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection

et al. 2022

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Herpes simplex virus-1 (HSV-1) is a large, enveloped DNA virus and its assembly in the cell is a complex multi-step process during which viral particles interact with numerous cellular compartments such as the nucleus and organelles of the secretory pathway. Transmission electron microscopy and fluorescence microscopy are commonly used to study HSV-1 infection. However, 2D imaging limits our understanding of the 3D geometric changes to cellular compartments that accompany infection and sample processing can introduce morphological artefacts that complicate interpretation. In this study, we used soft X-ray tomography to observe differences in whole-cell architecture between HSV-1 infected and uninfected cells. To protect the near-native structure of cellular compartments we used a non-disruptive sample preparation technique involving rapid cryopreservation, and a fluorescent reporter virus was used to facilitate correlation of structural changes with the stage of infection in individual cells. We observed viral capsids and assembly intermediates interacting with nuclear and cytoplasmic membranes. Additionally, we observed differences in the morphology of specific organelles between uninfected and infected cells. The local concentration of cytoplasmic vesicles at the juxtanuclear compartment increased and their mean width decreased as infection proceeded, and lipid droplets transiently increased in size. Furthermore, mitochondria in infected cells were elongated and highly branched, suggesting that HSV-1 infection alters the dynamics of mitochondrial fission/fusion. Our results demonstrate that high-resolution 3D images of cellular compartments can be captured in a near-native state using soft X-ray tomography and have revealed that infection causes striking changes to the morphology of intracellular organelles.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection

et al. 2022

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“…Data obtained from the same heart are indicated by color and presented as either individual points or as violin superplots including information on data heterogeneity—the normalized density estimates of individual replicates are stacked to show how each replicate (color-coded area) contributes to the overall density estimate (outline) [ 16 ]; all graphs additionally indicate the mean ± standard error of the mean (SEM). Statistical significance of data was assessed based on mean values of all daily recordings to avoid pseudo-replication.…”

Section: Methodsmentioning

confidence: 99%

Consecutive-Day Ventricular and Atrial Cardiomyocyte Isolations from the Same Heart: Shifting the Cost–Benefit Balance of Cardiac Primary Cell Research

Greiner

Schiatti

Kaltenbacher

et al. 2022

Cells

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Freshly isolated primary cardiomyocytes (CM) are indispensable for cardiac research. Experimental CM research is generally incompatible with life of the donor animal, while human heart samples are usually small and scarce. CM isolation from animal hearts, traditionally performed by coronary artery perfusion of enzymes, liberates millions of cells from the heart. However, due to progressive cell remodeling following isolation, freshly isolated primary CM need to be used within 4–8 h post-isolation for most functional assays, meaning that the majority of cells is essentially wasted. In addition, coronary perfusion-based isolation cannot easily be applied to human tissue biopsies, and it does not straightforwardly allow for assessment of regional differences in CM function within the same heart. Here, we provide a method of multi-day CM isolation from one animal heart, yielding calcium-tolerant ventricular and atrial CM. This is based on cell isolation from cardiac tissue slices following repeated (usually overnight) storage of the tissue under conditions that prolong CM viability beyond the day of organ excision by two additional days. The maintenance of cells in their near-native microenvironment slows the otherwise rapid structural and functional decline seen in isolated CM during attempts for prolonged storage or culture. Multi-day slice-based CM isolation increases the amount of useful information gained per animal heart, improving reproducibility and reducing the number of experimental animals required in basic cardiac research. It also opens the doors to novel experimental designs, including exploring same-heart regional differences.

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“…Finally, one of the exceptional features of R is that it can overlap not only text (in the previous examples, the outputs of statistical tests) with graphics, but also several graphical layers. In the following example, the three distributions are shown using three tracks: standard box plots [ 51 ], beeswarm plots [ 52 ] and violin plots [ 53 ] in order to fully assess the features of the distributions. The and functions require the homonymous CRAN packages.…”

Section: Practical Rmentioning

confidence: 99%

The R Language: An Engine for Bioinformatics and Data Science

Giorgi

Ceraolo

Mercatelli

2022

Life

105

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The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, and its community has produced tens of thousands of extensions and packages, with scopes ranging from machine learning to transcriptome data analysis. In this review, we provide an historical chronicle of how R became what it is today, describing all its current features and capabilities. We also illustrate the major tools of R, such as the current R editors and integrated development environments (IDEs), the R Shiny web server, the R methods for machine learning, and its relationship with other programming languages. We also discuss the role of R in science in general as a driver for reproducibility. Overall, we hope to provide both a complete snapshot of R today and a practical compendium of the major features and applications of this programming language.

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Violin SuperPlots: visualizing replicate heterogeneity in large data sets

Cited by 33 publications

References 12 publications

Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection

Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection

Consecutive-Day Ventricular and Atrial Cardiomyocyte Isolations from the Same Heart: Shifting the Cost–Benefit Balance of Cardiac Primary Cell Research

The R Language: An Engine for Bioinformatics and Data Science

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