# Omics data visualization in R and Python

## Omics data visualization in R and Python

- [From Authors](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/from-authors.md): Before you dive into this book
- [Virtual environments - let's begin](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/virtual-environments-lets-begin.md): What are virtual environments and why do we need them, Anaconda | Conda
- [Getting started with Python](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/getting-started-with-python.md): Installation of Python, Pycharm, Jupyter Notebook, Google Colab, and Python repositories and libraries
- [Getting started with R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/getting-started-with-r.md): Installation of R, RStudio, Jupyter Notebook, RMarkdown, Google Colab, R libraries and packages
- [Example data sets](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/example-data-sets.md): Data set for computations and visualizations used in this Gitbook
- [Data set from ISC Prague 2026](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/introduction/data-set-from-isc-prague-2026.md)
- [Fundamental data structures](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/fundamental-data-structures.md): A part of preparing data for analysis and visualization in OMICs analysis
- [Loading data into R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/loading-data-into-r.md): A part of preparing data for analysis and visualization for OMICs analysis
- [Preferred formats in metabolomics and lipidomics analysis](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/preferred-formats-in-metabolomics-and-lipidomics-analysis.md): A part of preparing data for analysis and visualization in OMICs analysis
- [Preprocess data type using Tidyverse package](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/preprocess-data-type-using-tidyverse-package.md): A part of preparing data for analysis and visualization in OMICs analysis
- [Useful R tricks and features in OMICs mining](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/useful-r-tricks-and-features-in-omics-mining.md): A part of preparing data for analysis and visualization
- [Application of pipe (%>%) functions](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/useful-r-tricks-and-features-in-omics-mining/application-of-pipe-greater-than-functions.md): Useful tricks and features in OMICs mining
- [Changing data frames format with pivot\_longer()](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/useful-r-tricks-and-features-in-omics-mining/changing-data-frames-format-with-pivot_longer.md): Useful tricks and features in OMICs mining
- [Data wrangling syntaxes useful in OMICs mining](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/useful-r-tricks-and-features-in-omics-mining/data-wrangling-syntaxes-useful-in-omics-mining.md): Useful tricks and features in OMICs mining
- [Writing functions in R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/useful-r-tricks-and-features-in-omics-mining/writing-functions-in-r.md): Useful tricks and features in OMICs mining
- [The 'for' loop in R (advanced)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-r/useful-r-tricks-and-features-in-omics-mining/the-for-loop-in-r-advanced.md): Useful tricks and features in OMICs mining
- [Fundamental data structures](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-python/fundamental-data-structures.md): Python has several built-in primitive data types, the most important for data analysis being:
- [Loading data into Python](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/performing-fundamental-operations-on-omics-data-using-python/loading-data-into-python.md)
- [Missing values – Introduction](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/missing-values-introduction.md): A part of missing values section
- [Detecting missing values (DataExplorer R package)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/detecting-missing-values-dataexplorer-r-package.md): A part of preparing data for statistical analysis and visualization
- [Filtering out columns containing mostly NAs](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/filtering-out-columns-containing-mostly-nas.md): A part of missing values section
- [Data imputation by different available R libraries](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/data-imputation-by-different-available-r-libraries.md): A part of missing values section
- [Basic data imputation in R with dplyr and tidyr (tidyverse)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/data-imputation-by-different-available-r-libraries/basic-data-imputation-in-r-with-dplyr-and-tidyr-tidyverse.md): A part of missing value – data imputation section
- [Data imputation using recipes library (tidymodels)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/data-imputation-by-different-available-r-libraries/data-imputation-using-recipes-library-tidymodels.md): A part of missing value – data imputation section
- [Replacing NAs via k-nearest neighbor (kNN) model (VIM library)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/data-imputation-by-different-available-r-libraries/replacing-nas-via-k-nearest-neighbor-knn-model-vim-library.md): A part of missing value – data imputation section
- [Replacing NAs via random forest (RF) model (randomForest library)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-r/data-imputation-by-different-available-r-libraries/replacing-nas-via-random-forest-rf-model-randomforest-library.md): A part of missing value – data imputation section
- [Detecting missing values](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-python/detecting-missing-values.md)
- [Filtering out columns containing mostly NAs](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-python/filtering-out-columns-containing-mostly-nas.md)
- [Data imputation](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/missing-values-handling-in-python/data-imputation.md)
- [Data normalization in R - fundamentals](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-normalization-in-r-fundamentals.md): A part of data transformation & normalization
- [Data normalization to the internal standards (advanced)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-normalization-to-the-internal-standards-advanced.md): A part of data transformation & normalization
- [Batch effect corrections in R (advanced)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/batch-effect-corrections-in-r-advanced.md): A part of preprocessing data as transformation & normalization
- [Data transformation and scaling - introduction](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-transformation-and-scaling-introduction.md): A part of data transformation & normalization
- [Data transformation and scaling using different available R packages](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-transformation-and-scaling-using-different-available-r-packages.md): A part of data transformation & normalization
- [Data transformation and scaling using mutate()](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-transformation-and-scaling-using-different-available-r-packages/data-transformation-and-scaling-using-mutate.md): A part of data transformation & normalization – using available R packages
- [Data transformation and scaling using recipes R package](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-transformation-and-scaling-using-different-available-r-packages/data-transformation-and-scaling-using-recipes-r-package.md): A part of data transformation & normalization – using available R packages
- [Data Normalization – bestNormalize R package](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-r/data-transformation-and-scaling-using-different-available-r-packages/data-normalization-bestnormalize-r-package.md): A part of data transformation & normalization – using available R packages
- [Data Transformation and scaling in Python](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/data-transformation-scaling-and-normalization-in-python/data-transformation-and-scaling-in-python.md)
- [Computing descriptive statistics in R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/computing-descriptive-statistics-in-r.md): Metabolites and lipids descriptive statistical analysis in R
- [Using gtsummary to create publication-ready tables](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/using-gtsummary-to-create-publication-ready-tables.md): Metabolites and lipids descriptive statistical analysis in R
- [Basic plotting in R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r.md): Metabolites and lipids descriptive statistical analysis in R
- [Bar charts](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/bar-charts.md): Metabolites and lipids descriptive statistical analysis in R
- [Box plots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/box-plots.md): Metabolites and lipids descriptive statistical analysis in R
- [Histograms](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/histograms.md): Metabolites and lipids descriptive statistical analysis in R
- [Density plots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/density-plots.md): Metabolites and lipids descriptive statistical analysis in R
- [Scatter plots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/scatter-plots.md): Metabolites and lipids descriptive statistical analysis in R
- [Dot plots with ggplot2 and tidyplots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/dot-plots-with-ggplot2-and-tidyplots.md): Metabolites and lipids descriptive statistical analysis in R
- [Correlation heat maps](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r/correlation-heat-maps.md): Metabolites and lipids descriptive statistical analysis in R
- [Customizing ggpubr and ggplot2 charts in R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/customizing-ggpubr-and-ggplot2-charts-in-r.md): Metabolites and lipids descriptive statistical analysis in R
- [Creating interactive plots with ggplotly](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/creating-interactive-plots-with-ggplotly.md): Metabolites and lipids descriptive statistical analysis in R
- [GGally for quick overviews](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/ggally-for-quick-overviews.md): Metabolites and lipids descriptive statistical analysis in R
- [Basic plotting](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistics-analysis-in-python/basic-plotting.md)
- [Scatter plots and linear regression](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistics-analysis-in-python/scatter-plots-and-linear-regression.md)
- [Correlation analysis](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistics-analysis-in-python/correlation-analysis.md)
- [Two sample comparisons in R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/two-sample-comparisons-in-r.md): Metabolites and lipids univariate statistical analysis in R
- [Multi sample comparisons in R](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/multi-sample-comparisons-in-r.md): Metabolites and lipids univariate statistical analysis in R
- [Adjustments of p-values for multiple comparisons](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/adjustments-of-p-values-for-multiple-comparisons.md): Metabolites and lipids univariate statistical analysis in R
- [Effect size computation and interpretation](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/effect-size-computation-and-interpretation.md): Metabolites and lipids univariate statistical analysis in R
- [Graphical representation of univariate statistics](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/graphical-representation-of-univariate-statistics.md): Metabolites and lipids univariate statistical analysis in R
- [Results of tests as annotations in the charts](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/graphical-representation-of-univariate-statistics/results-of-tests-as-annotations-in-the-charts.md): Metabolites and lipids univariate statistical analysis in R
- [Volcano plots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/graphical-representation-of-univariate-statistics/volcano-plots.md): Metabolites and lipids univariate statistical analysis in R
- [Lipid maps and acyl-chain plots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistics-in-r/graphical-representation-of-univariate-statistics/lipid-maps-and-acyl-chain-plots.md): Metabolites and lipids univariate statistical analysis in R
- [Two sample comparisons in Python](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistical-analysis-in-python/two-sample-comparisons-in-python.md)
- [Multi-sample comparisons in Python](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistical-analysis-in-python/multi-sample-comparisons-in-python.md)
- [Statistical annotations on plots](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-univariate-statistical-analysis-in-python/statistical-annotations-on-plots.md)
- [Principal Component Analysis (PCA)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/principal-component-analysis-pca.md): Metabolites and lipids multivariate statistical analysis in R
- [t-Distributed Stochastic Neighbor Embedding (t-SNE)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/t-distributed-stochastic-neighbor-embedding-t-sne.md): Metabolites and lipids multivariate statistical analysis in R
- [Uniform Manifold Approximation and Projection (UMAP)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/uniform-manifold-approximation-and-projection-umap.md): Metabolites and lipids multivariate statistical analysis in R
- [Partial Least Squares (PLS)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/partial-least-squares-pls.md): Metabolites and lipids multivariate statistical analysis in R
- [Orthogonal Partial Least Squares (OPLS)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/orthogonal-partial-least-squares-opls.md): Metabolites and lipids multivariate statistical analysis in R
- [Hierarchical Clustering (HC)](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/hierarchical-clustering-hc.md): Metabolites and lipids multivariate statistical analysis in R
- [Dendrograms](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/hierarchical-clustering-hc/dendrograms.md): Metabolites and lipids multivariate statistical analysis in R
- [Heat maps with clustering](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/hierarchical-clustering-hc/heat-maps-with-clustering.md): Metabolites and lipids multivariate statistical analysis in R
- [Interactive heat maps](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-r/hierarchical-clustering-hc/interactive-heat-maps.md): Metabolites and lipids multivariate statistical analysis in R
- [Principal Component Analysis](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-python/principal-component-analysis.md)
- [t-Distributed Stochastic Neighbor Embedding](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-python/t-distributed-stochastic-neighbor-embedding.md)
- [Uniform Manifold Approximation and Projection](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-python/uniform-manifold-approximation-and-projection.md)
- [PLS Discriminant Analysis](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-python/pls-discriminant-analysis.md)
- [Clustered heatmaps](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-multivariate-statistical-analysis-in-python/clustered-heatmaps.md)
- [Application of selected models to OMICs data](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/omics-in-machine-learning-approaches-in-r-and-python/application-of-selected-models-to-omics-data.md): Elements of machine learning using OMICs data
- [OMICs machine learning – Examples](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/omics-in-machine-learning-approaches-in-r-and-python/omics-machine-learning-examples.md): Elements of machine learning using OMICs data
- [Library versions](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/references/library-versions.md)