There exist many tools that can make your life easier when creating figures, and knowing a few of them can save you a lot of time. Depending on the type of visual you're trying to create, there is generally a dedicated tool that will do what you're trying to achieve.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.
Permits to conduct comparative analysis of any type of biological information that can be represented in both symmetrical and asymmetrical matrix form. iVici is an application that permits simultaneous visualization and correlation of multiple datasets. This application provides three visualization modes: general, comparative and superimposed. It uses combinations of colors to represent datasets and color scale rendering of matrix values, allowing quick identification of regions of data intersection.
Allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as a file or by copy-pasteing it to the text box. Data format is shown under "Help" tab. Several R packages are used internally, including shiny, ggplot2, pheatmap, RColorBrewer, FactoMineR, pcaMethods, shinyBS and others.
An R package for declaratively creating graphics. Ggplot2 allows to produce complex multi-layered graphics. Ggplot2 can create statistical graphics easier with user-friendly wrappers and a rich set of components.
Allows network visualization. Cytoscape Web can be customized and incorporated into any web site. It allows the client application to define a network of nodes and edges and customize their attributes. The tool permits to dynamically change node and edge visual styles, using any of the following methods: specifying default visual properties for all elements; mapping node and edge attributes to visual styles; and overriding default or mapped styles by setting a bypass style.
Allows generation of highly customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams of two or three sets. VennDiagram allows drawing Euler diagrams using circles and/or ellipses with two or three sets and generation of high resolution TIFF files that are standard in publications. The software can assist the promotion of the usage of automatically generated Venn diagrams within computational pipelines.
Creates reusable, flexible, interactive charts that are highly customizable. Webcharts provides a method for creating commonly-used charts, including bar charts, scatterplots, and timelines, through a simple configuration scheme. It allows users to create reusable charts that range from simple static graphics to complex interactive data exploration tools with custom user interfaces, all using the same library.
An R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings.
Unites the Microsoft Excel spreadsheet and allows users to perform multivariate analysis and visualization. imDEV simplifies multivariate data interpretation by integrating dynamic data visualization with univariate statistics, dimensional reduction methods, predictive modeling and network analyses tools. In summary, this tool consists of a Visual Basic for Applications (VBA)-based graphical user interface that accesses R-based visualizations and statistical algorithms, that operate on data stored within and returned to named ranges or worksheets within Excel.
Analyzes data using predefined analysis scenarios via a graphical user interface (GUI). RReportGenerator is a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. It allows calling R and executing the code from a user-selected pre-defined ‘Analysis Scenario’ for automatically generating reports. RReportGenerator can be used in a wide range of routine analysis cases in clinical and biological research where the aim and structure of the experiments change rarely, like automatic quality control (e.g. of Affymetrix arrays) or analyzing high content screening (HCS) plates.
Enables rapid and automatic generation of TEX encoded graphics from SBML files with layout and rendering information. SBML2TikZ is an application that performs all essential rendering functions such as scaling, page size selection and accurate graph generation automatically. This application can be run from either a graphical user interface (GUI) or from a console.
Allows users to encode metadata as edge colors of a given graph. graph_annotation is an application dedicated to the management and edition of individual annotation tracks to a given graph structure. This program enables a dynamic addition of data and a modular combination of multiple colors as well as changes in underlying structures and a double compression with both wavelets tries and Bloom filters.
TeX packages for creating graphics programmatically. TikZ is build on top of PGF and allows you to create sophisticated graphics in a rather intuitive and easy manner. TikZ offers all the advantages of the “TEX-approach to typesetting” for graphics: quick creation of simple graphics, precise positioning, the use of macros, often superior typography. PGF is a TeX macro package for generating graphics. It is platform- and format-independent and works together with the most important TeX backend drivers, including pdftex and dvips.
Allows combined integration and visualization of molecular expression data in some vertebrate model organisms. COMICS employs pre-existing anatomical ontologies to map arbitrary omics data across experiments. It produces custom, publication-quality, vector graphics mapping molecular expression data to anatomical diagrams. This tool provides an interface that allows users to select the appropriate visual representation and export publication-quality graphics.
Provides assistance to determine optimal combinations of markers from diverse complex omics data. CombiROC uses combinatorial analysis and receiving operator characteristic (ROC) curves to perform. It works through two-steps: first a combinatorial analysis that computes all the possible combinations of markers given a set of constraints and optional data transformation. It then computes and evaluates sensitivity and specificity of all marker combinations and ROC combinations.
Allows addition of a substantial list of customizable sparklines to tabular data representations. JSparklines is a Java library that expands on sparklines concept by including any type of cell-size graphic that can be used to improve the understanding of the underlying data. This includes bar charts, area charts, line charts, box plots and scatter plots, along with simpler options such as equally sized, colored boxes to represent groups or categories.
Extends the 3-dimensional function of the 1-dimensional boxplots and the 2-dimensional bagplot. gemPlot is based on use a three-dimensional array that lays a 3D grid across the data points in order to determine the sets Dk in the three-dimensional space. It outperforms the other two approaches with respect to specificity and in the detection of false positive results. The tool is objective and provides an automated detection of outliers.
Provides an implementation of the Johnson-Neyman (JN) technique. CAHOST consists of 6 sheets in a Microsoft Excel 2013 macro-enabled workbook. The JN technique is a method for exploring the moderating effect that a continuous variable has on the relationship between a focal predictor and the response variable. This workbook produces publication-ready graphics, requires no programming capabilities, and limits error in data entry. It also automates the linear regression.