de.jstacs.utils
Class SeqLogoPlotter

java.lang.Object
  de.jstacs.utils.SeqLogoPlotter

public class SeqLogoPlotter
extends Object

Class with static methods for plotting sequence logos of DNA motifs, i.e., position weight matrices defined over a DNAAlphabet. In general, sequence logos can be plotted to any Graphics2D object, e.g., for on-screen printing using the plotLogo methods. For convenience, the method plotLogoToPNG(String, int, double[][]) can be used to directly plot a sequence logo to a PNG file with a given height and automatically chosen aspect ratio.

Author:

Jan Grau

Constructor Summary

SeqLogoPlotter()

Method Summary

protected static Pair<BufferedImage,Graphics2D>	getBufferedImageAndGraphics(int height, double[][] ps) Creates a new BufferedImage with given height and width chosen automatically according to the number of rows of ps, and returns this BufferedImage and its Graphics2D object.
static int	getHeight(int width, double[][] ps) Returns the automatically chosen height for a given width and position weight matrix.
static int	getWidth(int height, double[][] ps) Returns the automatically chosen width for a given height and position weight matrix.
static void	plotLogo(Graphics2D g, int h, double[][] ps) Plots the sequence logo for the position weight matrix given in ps.
static void	plotLogo(Graphics2D g, int height, double[][] ps, String[] labels, String labX, String labY) Plots the sequence logo for the position weight matrix given in ps.
static void	plotLogo(Graphics2D g, int w, int h, double[][] ps, String[] labels, String labX, String labY) Plots the sequence logo for the position weight matrix given in ps.
static void	plotLogo(Graphics2D g, int x, int y, int w, int h, double[][] ps, String[] labels, String labX, String labY) Plots the sequence logo for the position weight matrix given in ps.
static BufferedImage	plotLogoToBufferedImage(int height, double[][] ps) Plots the sequence logo for the position weight matrix given in ps.
static void	plotLogoToPNG(String path, int height, double[][] ps) Plots the sequence logo for the position weight matrix given in ps.
static void	plotTALgetterLogo(Graphics2D g, int x, int y, int w, int h, double[][] ps, double[] imp, String[] labels, String labX, String labY, String labY2) Plots the TALgetter logo for the binding specificities given in ps.
static BufferedImage	plotTALgetterLogoToBufferedImage(int height, double[][] ps, double[] imp, String[] lab) Plots the TALgetter logo for the binding specificities given in ps.
static void	plotTALgetterLogoToPNG(String path, int height, double[][] ps, double[] imp, String[] lab) Plots the TALgetter logo for the binding specificities given in ps.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SeqLogoPlotter

public SeqLogoPlotter()

Method Detail

plotLogoToPNG

public static void plotLogoToPNG(String path,
                                 int height,
                                 double[][] ps)
                          throws IOException

Plots the sequence logo for the position weight matrix given in ps. The rows of ps correspond to positions in the sequence logo. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. The positions of the sequence logo are numbered contiguously from 1 to ps.length. The label of the x-axis is set to "Position", and the label of the y-axis is set to "bits". The sequence logo is written to the PNG file given in path.

Parameters:

path - the path to the PNG file written

height - the height of the PNG image (in pixels)

ps - the position weight matrix

Throws:

IOException - if the file could not be written

plotLogoToBufferedImage

public static BufferedImage plotLogoToBufferedImage(int height,
                                                    double[][] ps)

Plots the sequence logo for the position weight matrix given in ps. The rows of ps correspond to positions in the sequence logo. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. The positions of the sequence logo are numbered contiguously from 1 to ps.length. The label of the x-axis is set to "Position", and the label of the y-axis is set to "bits". The sequence logo is return as a BufferedImage.

Parameters:

height - the height of the PNG image (in pixels)

ps - the position weight matrix

Returns:

the sequence logo

getBufferedImageAndGraphics

protected static Pair<BufferedImage,Graphics2D> getBufferedImageAndGraphics(int height,
                                                                            double[][] ps)

Creates a new BufferedImage with given height and width chosen automatically according to the number of rows of ps, and returns this BufferedImage and its Graphics2D object.

Parameters:

height - the height (in pixels)

ps - the position weight matrix

Returns:

the created BufferedImage and its Graphics2D object

plotLogo

public static void plotLogo(Graphics2D g,
                            int h,
                            double[][] ps)

Plots the sequence logo for the position weight matrix given in ps. The rows of ps correspond to positions in the sequence logo. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. The positions of the sequence logo are numbered contiguously from 1 to ps.length. The label of the x-axis is set to "Position", and the label of the y-axis is set to "bits". The sequence logo is written to the Graphics2D object given in g.

Parameters:

g - the Graphics2D object

h - the height of the sequence logo

ps - the position weight matrix

plotLogo

public static void plotLogo(Graphics2D g,
                            int height,
                            double[][] ps,
                            String[] labels,
                            String labX,
                            String labY)

Plots the sequence logo for the position weight matrix given in ps. The rows of ps correspond to positions in the sequence logo. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. The sequence logo is written to the Graphics2D object given in g.

Parameters:

g - the Graphics2D object

height - the height of the sequence logo

ps - the position weight matrix

labels - the labels of the positions of the sequence logo, if null the positions are numbered contiguously from 1 to ps.length

labX - the label of the x-axis

labY - the label of the y-axis

getWidth

public static int getWidth(int height,
                           double[][] ps)

Returns the automatically chosen width for a given height and position weight matrix.

Parameters:

height - the height

ps - the position weight matrix

Returns:

the width

getHeight

public static int getHeight(int width,
                            double[][] ps)

Returns the automatically chosen height for a given width and position weight matrix.

Parameters:

width - the width

ps - the position weight matrix

Returns:

the height

plotLogo

public static void plotLogo(Graphics2D g,
                            int w,
                            int h,
                            double[][] ps,
                            String[] labels,
                            String labX,
                            String labY)

Plots the sequence logo for the position weight matrix given in ps. The rows of ps correspond to positions in the sequence logo. Each row must be normalized. The sequence logo is written to the Graphics2D object given in g.

Parameters:

g - the Graphics2D object

w - the width of the sequence logo

h - the height of the sequence logo

ps - the position weight matrix

labels - the labels of the positions of the sequence logo, if null the positions are numbered contiguously from 1 to ps.length

labX - the label of the x-axis

labY - the label of the y-axis

plotLogo

public static void plotLogo(Graphics2D g,
                            int x,
                            int y,
                            int w,
                            int h,
                            double[][] ps,
                            String[] labels,
                            String labX,
                            String labY)

Plots the sequence logo for the position weight matrix given in ps. The rows of ps correspond to positions in the sequence logo. Each row must be normalized. The sequence logo is written to the Graphics2D object given in g.

Parameters:

g - the Graphics2D object

x - the x-coordinate of the bottom left corner of the sequence logo

y - the y-coordinate of the bottom left corner of the sequence logo (-h results in a sequence logo spanning from 0 to h)

w - the width of the sequence logo

h - the height of the sequence logo

ps - the position weight matrix

labels - the labels of the positions of the sequence logo, if null the positions are numbered contiguously from 1 to ps.length

labX - the label of the x-axis

labY - the label of the y-axis

plotTALgetterLogoToPNG

public static void plotTALgetterLogoToPNG(String path,
                                          int height,
                                          double[][] ps,
                                          double[] imp,
                                          String[] lab)
                                   throws IOException

Plots the TALgetter logo for the binding specificities given in ps. The rows of ps correspond to specificities of the RVDs. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. In addition, the importance of RVDs is plotted as given in imp. The labels of the RVDs are given in lab. The label of the x-axis is set to "RVD", and the label of the y-axes are set to "bits" and "Importance", respectively. The TALgetter logo is written to the PNG file given in path.

Parameters:

path - the path to the PNG file written

height - the height of the PNG image (in pixels)

ps - the binding specificities of RVDs

imp - the importance of RVDs

lab - the amino acids of the RVDs in one-letter code

Throws:

IOException - if the file could not be written

plotTALgetterLogoToBufferedImage

public static BufferedImage plotTALgetterLogoToBufferedImage(int height,
                                                             double[][] ps,
                                                             double[] imp,
                                                             String[] lab)

Plots the TALgetter logo for the binding specificities given in ps. The rows of ps correspond to specificities of the RVDs. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. In addition, the importance of RVDs is plotted as given in imp. The labels of the RVDs are given in lab. The label of the x-axis is set to "RVD", and the label of the y-axes are set to "bits" and "Importance", respectively. The TALgetter logo is returned as BufferedImage.

Parameters:

height - the height of the PNG image (in pixels)

ps - the binding specificities of RVDs

imp - the importance of RVDs

lab - the amino acids of the RVDs in one-letter code

Returns:

the TALgetter logo

plotTALgetterLogo

public static void plotTALgetterLogo(Graphics2D g,
                                     int x,
                                     int y,
                                     int w,
                                     int h,
                                     double[][] ps,
                                     double[] imp,
                                     String[] labels,
                                     String labX,
                                     String labY,
                                     String labY2)

Plots the TALgetter logo for the binding specificities given in ps. The rows of ps correspond to specificities of the RVDs. Each row must be normalized. For a given height (in pixels), the width is chosen automatically depending on the number of rows in ps. In addition, the importance of RVDs is plotted as given in imp. The labels of the RVDs are given in lab. The label of the x-axis is set to "RVD", and the label of the y-axes are set to "bits" and "Importance", respectively. The TALgetter logo is returned as BufferedImage.

Parameters:

g - the Graphics2D object

x - the x-coordinate of the bottom left corner of the TALgetter logo

y - the y-coordinate of the bottom left corner of the TALgetter logo (-h results in a logo spanning from 0 to h)

w - the width of the TALgetter logo

h - the height of the TALgetter logo

ps - the binding specificities of RVDs

imp - the importance of RVDs

labels - the amino acids of the RVDs in one-letter code

labX - the label of the x-axis

labY - the label of the y-axis

labY2 - the label of the second (importance) y-axis