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FIESTA 2.0 | BioinfoGP | CNB | CSIC

FIESTA 2.0: Interactive Scatter Plots

Manual

Introduction

FIESTA Viewer consists on a single html file compatible with any modern web browser. All data and functions are fully integrated in the viewer so you do not need an internet connection or other resources to navigate your results.

As all computations are made inside your computer, for the viewer to run smoothly, a minimum of 4GB RAM and a 4-core processor is required.

In the following sections, FIESTA capabilities will be illustrated with this example corresponding to a parcial re-analysis of a published RNA-Seq project by Hakkaart X et al. (2020). In this example, each data row represents a Saccharomyces cerevisiae gene and there are columns for gene expression values, P-values, gene symbols, gene descriptions, etc.

NOTE: FIESTA Viewer is, in no way, restricted to RNA-Seq results. You can use it to navigate any kind of dataset stored in a standard file (tabulated-text or MS Excel) suitable to be represented as scatter plot. As of 2022, FIESTA may handle tables of up to ~300,000 data rows and up to ~30 columns of numerical and textual data (symbols, descriptions, etc.) on an average computer.

To open FIESTA Viewer in your default browser, double-click the html file.

FIESTA interface can be divided in three main areas:

  • Left: Scatter Plot
  • Bottom: Data Table
  • Right: Data Subsets

FIESTA Viewer showing the Scatter Plot at left, the Data Table at bottom and the Data Subsets (only the default "All values") at right.

Scatter Plot

In FIESTA Viewer, data is represented graphically in form of scatter plots. You can represent several data subsets, zoom-in to interesting areas, select individual spots, modify axes scales, etc.

To set the data columns for horizontal (x) and vertical (y) axes, click on Data Source. In the dialog, select the desired columns for each axis and, optionally, select also columns for horizontal and vertical error bars. Yo can set axes's limits manually or click Auto Scale to set them automatically. Click Apply to update the plot or Cancel to discard current selections.

Dialog to choose columns for scatter plot axes and error bars.

You can modify the appearance of the axes by using the small buttons next to them. You can reverse the values, set the axis scale as log10, log2, log or raw, and to increase/decrease the number of axis labels (ticks).

Plotting "log2Ratio(pH3/pH5)" column versus "P-adjusted" column in reverse order and in log10 scale.

To zoom-in the plot, drag the desired area with the mouse. To show the full plot again, click Reset Zoom.

Select any spot by clicking on it. Click again on a selected spot to deselect it.

Zoomed-in plot with several spots selected by hand (clicked).

You can decrease/increase the spot's size by clicking one of the two small circles at upper-left.

You can save the plot, as a high-resolution png image, by clicking Save Plot.

Data Table

The source data is shown as a paginated table in this area. You can sort the rows by any column, select/deselect individual rows and filter them by one or several criteria (numerical or textual).

To sort the data rows by a given column, click the corresponding header's caption. Click again to invert the sense.

To select an individual row, double-click on it. The data in this row will be incorporated to the "Selected by hand" subset. To deselect it, double-click on it again.

To filter data, write one or several criteria in the desired header's filtering boxes and press Enter. For example: to select genes with "P-adjusted" lower than 0.05 and positive log2Ratios, write down "< 0.05" (without quotes) in the filtering box of "P-adjusted" column, write down "> 0" in the filtering box of "log2Ratio(pH3/pH5)" and press Enter. A new subset will show up and the table's header color will match its color.

Applying numerical filters to create a data subset.

Similarly, to create a new subset with genes with "P-adjusted" lower than 0.05 and negative log2Ratios, click on "All values" subset (above) and write down the corresponding filters in the filtering boxes.

Additional data subsets can be created by applying new filters to "All values".

Numerical filters can be set using "<", ">", "<=", ">=" and "=" operators.

You can also use textual filters. For example, to create a subset with genes containing "mannoprotein" in their descriptions, write down "mannoprotein" in the filtering box of "Gene description" column and press Enter. Textual filters are not case sensitive.

Applying textual filters to create a new data subset.

Textual filters can be used to search exact terms using "=" operator. For example, to get the genes of type "protein_coding", write down "=protein_coding" in the filtering box of "Gene type" column" and press Enter.

Finally, you can construct more complex filters by using "AND" and "OR" inside a single filtering box. For example, to generate a new subset with all genes with log2Ratio lower than -1 or log2Ratio greater than 1, write down "< -1 OR > 1" in the filtering box of column "log2Ratio(pH3/pH5)" and press Enter. You can even combine numerical and textual filters.

Numerical and textual filters can be combined.

Data Subsets

Here, details of both, manually selected data and filtered data are shown as data subsets. You can change their colors, re-order them, hide them and deleting them.

By default, only the subset "All values" is shown, indicating the number of total data rows in the source table.

Additional data subsets can be re-ordered by clicking on the small up/down arrows at right. This is useful to properly represent partially overlapping subsets in the scatter plot as the subsets are plotted in the same order in which they appear in the list.

The buttons at right are to organize and save data subsets.

You can change the subset's color by clicking the colored circle at left and pick a new one from the palette.

Selecting a new color for the subset.

To select a data subset, click on its description. The selected data will be shown in the table below. To help you to know which data subset is shown in the current table, the header's color always match with the selected subset.

To show/hide a subset in the scatter plot, click the corresponding checkbox.

You can delete a data subset by clicking the X at right.

Finally, you can export any data subset as tabulated-text file by clicking the corresponding Save button at right.

Credits and Acknowledgements

Developed by Juan Carlos Oliveros at BioinfoGP (CNB-CSIC).

FIESTA 2.0 contains many requests and suggestions by numerous life-sciences researchers and students that, over the last years, utilized previous versions of the tool to analyze their gene expression results.

Special THANKS to my BioinfoGP colleagues Juan Antonio García-Martín and Rafael Torres-Pérez for their suggestions and, above all, for their constructive criticism.

Please cite:

Oliveros JC. FIESTA 2.0: Interactive Scatter Plots in your Browser. (2022)
https://bioinfogp.cnb.csic.es/tools/fiesta2