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ggpubr - 'ggplot2' Based Publication Ready Plots

The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots require some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'-based publication ready plots. This version adds publication-ready figures for common analysis workflows: ROC curves with the area under the curve and its confidence interval ('ggrocplot()'), one- and two-way group comparison figures with brackets and an omnibus label ('ggcompare()'), volcano plots ('ggvolcano()'), forest and estimation plots ('ggestimates()'), raincloud plots ('ggraincloud()'), compact letter displays ('stat_cld()') and test labels ('add_test_label()'), together with automatic bracket packing for pairwise comparisons ('geom_pwc()').

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19.70 score 1.3k stars 510 dependents 104k scripts 206k downloads

rstatix - Pipe-Friendly Framework for Basic Statistical Tests

Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs (repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs. It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and 'Cramer V' for the association between categorical variables. The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.

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17.56 score 493 stars 532 dependents 15k scripts 220k downloads

factoextra - Extract and Visualize the Results of Multivariate Data Analyses

Provides easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis), and 'HMFA' (Hierarchical Multiple Factor Analysis) from different R packages. It standardizes coordinates, squared cosines, contributions, and eigenvalues from several analysis backends and produces 'ggplot2'-based factor maps, scree plots, contribution plots, clustering diagnostics, dendrograms, and silhouette plots. It also visualizes two-dimensional 'UMAP' and t-SNE embeddings and adapts precomputed or 'tidymodels' principal-component results for the same plotting interface.

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16.38 score 386 stars 61 dependents 24k scripts 81k downloads

survminer - Drawing Survival Curves using 'ggplot2'

Contains the function 'ggsurvplot()' for drawing easily beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.

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15.32 score 575 stars 68 dependents 105 scripts 40k downloads

ggcorrplot - Visualization of a Correlation Matrix using 'ggplot2'

The 'ggcorrplot' package can be used to visualize easily a correlation matrix using 'ggplot2'. It provides a solution for reordering the correlation matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.

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14.72 score 197 stars 26 dependents 9.1k scripts 23k downloads

datarium - Data Bank for Statistical Analysis and Visualization

Contains data organized by topics: categorical data, regression model, means comparisons, independent and repeated measures ANOVA, mixed ANOVA and ANCOVA. The package code is under GPL-2; the data sets are covered by the terms in the 'LICENSE.note' file (the author's data sets under CC0 1.0, and the 'heartdisease' data under CC BY 4.0, see the 'heartdisease' help page).

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6.71 score 26 stars 401 scripts 3.3k downloads

fastqcr - Quality Control of Sequencing Data

'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing data. It produces, for each sample, an html report and a compressed file containing the raw data. If you have hundreds of samples, you are not going to open up each 'HTML' page. You need some way of looking at these data in aggregate. 'fastqcr' Provides helper functions to easily parse, aggregate and analyze 'FastQC' reports for large numbers of samples. It provides a convenient solution for building a 'Multi-QC' report, as well as, a 'one-sample' report with result interpretations.

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6.71 score 78 stars 1 dependents 146 scripts 627 downloads