mavolcanoplot

Create significance versus gene expression ratio (fold change) scatter plot of microarray data

Syntax

mavolcanoplot(DataX,DataY,PValues)

SigStructure = mavolcanoplot(DataX,DataY,PValues)

___ = mavolcanoplot(___,Name=Value)

Description

mavolcanoplot(DataX,DataY,PValues) creates a scatter plot of gene expression data, plotting significance versus fold change of gene expression ratios of two data sets, DataX and DataY. It plots significance as the -log₁₀ (p-value) from the input, PValues.

SigStructure = mavolcanoplot(DataX,DataY,PValues) returns a structure containing information for genes that are considered to be both statistically significant (above the p-value cutoff) and significantly differentially expressed (outside of the fold change values). The fields within SigStructure are sorted by p-value.

___ = mavolcanoplot(___,Name=Value) specifies options using one or more name-value arguments in addition to the input arguments in previous syntaxes. For example, to add labels for data points stored in myDataLabels, set Labels to myDataLabels.

Examples

Create Volcano Plot of Gene Expressions Related to Prostate Cancer

1. Load a MAT-file, included with the Bioinformatics Toolbox™ software, which contains Affymetrix^® data variables, including dependentData and independentData, two matrices of gene expression values from two experimental conditions.

   load prostatecancerexpdata

2. Use the mattest function to calculate p-values for the gene expression values in the two matrices.

   pvalues = mattest(dependentData, independentData);

3. Using the two matrices, the pvalues calculated by mattest, and the probesetIDs column vector of labels provided, use mavolcanoplot to create a significance versus gene expression ratio scatter plot of the microarray data from the two experimental conditions.

   mavolcanoplot(dependentData, independentData, pvalues,...
   'Labels', probesetIDs) 

4. View the volcano plot without the user interface components.

   mavolcanoplot(dependentData, independentData, pvalues,...
   'Labels', probesetIDs,'Plotonly', true) 

   

Input Arguments

DataX,DataY — Gene expression data

DataMatrix object | matrix | vector

Gene expression data specified as a DataMatrix object, matrix, or vector of gene expression from a single experimental condition. If specified as a DataMatrix object or a matrix, each row is a gene, each column is a sample, and an average expression value is calculated for each gene.

Note

If the values in DataX,DataY are natural scale, use the LogTrans property to convert them to log ₂ scale.

Example: mavolcanoplot(dependentData,independentData,pvals)

PValues — P-values for each feature in data set

vector of numerical values | DataMatrix object

P-values used to determine statistical significance of experimental data, specified as either a column vector or a DataMatrix object such as returned by the mattest function. The column vector or DataMatrix object contain p-values for each feature (for example, gene) in a data set.

Example: mavolcanoplot(dependentData,independentData,pvals)

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: mavolcanoplot(dependentData,independentData,pvals,'Labels',probesetIDs) labels the data points with the probe set IDs.

Labels — Data labels

character vector cell array | string vector

Cell array of character vectors or string vector containing labels (typically gene names or probe set IDs) for the data. After creating the plot, you can click a data point to display the label associated with it. If you do not specify the value of Labels, data points are labeled with row numbers from DataX,DataY.

Example: mavolcanoplot(dependentData,independentData,pvals,'Labels',probesetIDs)

LogTrans — Control data conversion

false (default) | true

Control the conversion of data in DataX,DataY from natural scale to log ₂ scale, specified as eithertrue or false.

• true — Converts data to log₂ scale.

• false — Assumes data is already log₂ scale, and the software does not perform a conversion.

Example: mavolcanoplot(dependentData,independentData,pvals,'LogTrans', true)

PCutoff — P-value statistical significance cutoff value

0.05 (default) | any numeric value between 0 and 1

The p-value to define data points that are statistically significant, specified as a numeric value. This value is displayed graphically as a horizontal line on the plot. Default is 0.05, which is equivalent to 1.3010 on the –log₁₀ (p-value) scale. The value must be between 0 and 1.

Note

You can also change the p-value cutoff interactively after creating the plot.

Example: mavolcanoplot(dependentData,independentData,pvals,'PCutoff',0.5)

Foldchange — Ratio fold change

2 (default) | numeric value

The ratio fold change to define data points that are differentially expressed specified as a numeric value that corresponds to a ratio of 1 and –1 on a log₂ (ratio) scale.

Note

You can also change the fold change interactively after creating the plot.

Example: mavolcanoplot(dependentData,independentData,pvals,'Foldchange',4)

PlotOnly — Display plot without user interface components

false (default) | true

Display of the volcano plot without user interface components specified as either true or false.

• false — Display the volcano plot with user interface components.

• true — Display the volcano plot without user interface components.

Note

If you set the PlotOnly argument to true, you can still display labels for data points by clicking a data point, and you can still adjust vertical fold change lines and the horizontal p-value cutoff line by click-dragging the lines.

Example: mavolcanoplot(dependentData,independentData,pvals,'PlotOnly',true)

Output Arguments

SigStructure — Structure of gene information

structure

Structure containing information for genes that are considered to be both statistically significant (above the p-value cutoff) and significantly differentially expressed (outside of the fold change values).

The fields within SigStructure are sorted by p-value and include:

• Name

• PCutoff

• FCThreshold

• GeneLabels

• PValues

• FoldChanges

Note

The fields PValues and FoldChanges will be either vectors or DataMatrix objects depending on the type of input PValues.

More About

Volcano Plot Key Features

The volcano plot displays the following:

• –log₁₀ (p-value) versus log₂ (ratio) scatter plot of genes

• Two vertical fold change lines at a fold change level of 2, which corresponds to a ratio of 1 and –1 on a log₂ (ratio) scale. (Lines will be at different fold change levels, if you used the Foldchange name-value argument.)

• One horizontal line at the 0.05 p-value level, which is equivalent to 1.3010 on the –log₁₀ (p-value) scale. (The line will be at a different p-value level, if you used the PCutoff name-value argument.)

Tips

After you display the volcano scatter plot, you can interactively:

• Adjust the vertical fold change lines by click-dragging one line or entering a value in the Fold Change text box.

• Adjust the horizontal p-value cutoff line by click-dragging or entering a value in the p-value Cutoff text box.

• Display labels for data points by clicking a data point.

• Select a gene from the Up Regulated or Down Regulated list to highlight the corresponding data point in the plot. Press and hold Ctrl or Shift to select multiple genes.

• Zoom the plot by selecting Tools > Zoom In or Tools > Zoom Out.

• View lists of significantly up-regulated and down-regulated genes and their associated p-values, and optionally, export the labels, p-values, and fold changes to a structure in the MATLAB^® Workspace by clicking Export.

References

[1] Cui, X., Churchill, G.A. (2003). Statistical tests for differential expression in cDNA microarray experiments. Genome Biology 4, 210.

[2] Best, C.J.M., Gillespie, J.W., Yi, Y., Chandramouli, G.V.R., Perlmutter, M.A., Gathright, Y., Erickson, H.S., Georgevich, L., Tangrea, M.A., Duray, P.H., Gonzalez, S., Velasco, A., Linehan, W.M., Matusik, R.J., Price, D.K., Figg, W.D., Emmert-Buck, M.R., and Chuaqui, R.F. (2005). Molecular alterations in primary prostate cancer after androgen ablation therapy. Clinical Cancer Research 11, 6823–6834.

Version History

Introduced in R2006a