Bioinformatics Toolbox™

chromosomeplot - Plot chromosome ideogram with G-banding pattern

Syntax

chromosomeplot(CytoData) chromosomeplot(CytoData, ChromNum) chromosomeplot(CytoData, ChromNum, ...,'Orientation', OrientationValue, ...) chromosomeplot(CytoData, ChromNum, ...,'ShowBandLabel', ShowBandLabelValue, ...) chromosomeplot(CytoData, ChromNum, ...,'AddToPlot', AddToPlotValue, ...) chromosomeplot(..., 'Unit', UnitValue, ...) chromosomeplot(..., 'CNV', CNVValue, ...)

Arguments

CytoData

Either of the following:

String specifying a file containing cytogenetic G-banding data (in bp units), such as an NCBI ideogram text file or a UCSC Genome Browser cytoband text file.
Structure containing cytogenetic G-banding data (in bp units) in the following fields:
- ChromLabels
- BandStartBPs
- BandEndBPs
- BandLabels
- GieStains

Tip Use the cytobandread function to create the structure to use for CytoData.

ChromNum

Scalar or string specifying a single chromosome to plot. Valid entries are integers, 'X', and 'Y'.

Note Setting ChromNum to 0 will plot ideograms for all chromosomes.

OrientationValue String or number that specifies the orientation of the ideogram of a single chromosome specified by ChromNum. Choices are 'Vertical' or 1 (default) and 'Horizontal' or 2.

ShowBandLabelValue Controls the display of band labels (such as q25.3) when plotting a single chromosome ideogram, specified by ChromNum. Choices are true (default) or false.

AddToPlotValue

Variable name of a figure axis to which to add the single chromosome ideogram, specified by ChromNum.

Note If you use this property to add the ideogram to a plot of genomic data that is in units other than bp, use the 'Unit' property to convert the ideogram data to the appropriate units.

Tip Before printing a figure containing an added chromosome ideogram, change the background to white by issuing the following command:

set(gcf,'color','w')

UnitValue Integer that specifies the units (base pairs, kilo base pairs, or mega base pairs) for the starting and ending genomic positions. This unit is used in the data tip displayed when you hover the cursor over chromosomes in the ideogram. This unit can also be used when using the 'AddToPlot' property to add the ideogram to a plot that is in units other than bp. Choices are 1 (bp), 2 (kb), or 3 (mb). Default is 1 (bp).

CNVValue Controls the display of copy number variance (CNV) data, provided by CNVValue, aligned to the chromosome ideogram. Gains are shown in green to the right or above the ideogram, while losses are shown in red to the left or below the ideogram. CNVValue is a structure array containing the four fields described in the table below.

Description

chromosomeplot(CytoData) plots the ideogram of all chromosomes, using information from CytoData, a structure containing cytogenetic G-banding data (in bp units), or a string specifying a file containing cytogenetic G-banding data (in bp units), such as an NCBI ideogram text file or a UCSC Genome Browser cytoband text file. The G bands distinguish different areas of the chromosome. For example, for the Homo sapiens ideogram, possible G bands are:

gneg — white
gpos25 — light gray
gpos50 — medium gray
gpos75 — dark gray
gpos100 — black
acen — red (centromere)
stalk — light blue (regions with repeats)
gvar — indented region

Darker bands are AT-rich, while lighter bands are GC-rich.

chromosomeplot(CytoData, ChromNum) plots the ideogram of a single chromosome specified by ChromNum.

chromosomeplot(..., 'PropertyName', PropertyValue, ...) calls chromosomeplot with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

chromosomeplot(CytoData, ChromNum, ...,'Orientation', OrientationValue, ...) specifies the orientation of the ideogram of a single chromosome specified by ChromNum. Choices are 'Vertical' or 1 (default) and 'Horizontal' or 2.

Note When plotting the ideogram of all chromosomes, the orientation is always vertical.

chromosomeplot(CytoData, ChromNum, ...,'ShowBandLabel', ShowBandLabelValue, ...) displays band labels (such as q25.3) when plotting a single chromosome ideogram, specified by ChromNum. Choices are true (default) or false.

chromosomeplot(CytoData, ChromNum, ...,'AddToPlot', AddToPlotValue, ...) adds the single chromosome ideogram, specified by ChromNum, to a figure axis specified by AddToPlotValue.

Note If you use this property to add the ideogram to a plot of genomic data that is in units other than bp, use the 'Unit' property to convert the ideogram data to the appropriate units.

Tip Before printing a figure containing an added chromosome ideogram, change the background to white by issuing the following command:

set(gcf,'color','w')

chromosomeplot(..., 'Unit', UnitValue, ...) specifies the units (base pairs, kilo base pairs, or mega base pairs) for the starting and ending genomic positions. This unit is used in the data tip displayed when you hover the cursor over chromosomes in the ideogram. This unit can also be used when using the 'AddToPlot' property to add the ideogram to a plot that is in units other than bp. Choices are 1 (bp), 2 (kb), or 3 (mb). Default is 1 (bp).

chromosomeplot(..., 'CNV', CNVValue, ...) displays copy number variance (CNV) data, provided by CNVValue, aligned to the chromosome ideogram. Gains are shown in green to the right or above the ideogram, while losses are shown in red to the left or below the ideogram. CNVValue is a structure array containing the following fields. Each field must contain the same number of elements.

Field Description

Chromosome

Either of the following:

Numeric vector containing the chromosome number on which each CNV is located.

Note For the sex chromosome, X, use N, where N = number of autosomes + 1. For the sex chromosome, Y, use M, where M = number of autosomes + 2. For example, for Homo sapiens use 23 for X and 24 for Y, and for Mus musculus (lab mouse), use 20 for X and 21 for Y.

Character array containing the chromosome number on which each CNV is located.

Note Using a character array lets you use the characters X and Y (instead of numbers) for sex chromosomes. However, all elements in the array must be the same width, which may require you to add spaces to the strings. For example:

[' 1'; ' 2'; '10'; ' X']

Or you can use the char function with a cell array to create a character array of the chromosome numbers and letters. For example: .

char({'1', '2', '10', 'X'})

CNVType

Numeric vector containing the type of each CNV, either 1 (loss) or 2 (gain).

Start

Numeric vector containing the starting genomic position of each CNV. Units must be in base pairs.

End

Numeric vector containing the ending genomic position of each CNV. Units must be in base pairs.

Examples

Plotting Chromosome Ideograms

Read the cytogenetic banding information for Homo sapiens into a structure.

hs_cytobands = cytobandread('hs_cytoBand.txt')

hs_cytobands = 

     ChromLabels: {862x1 cell}
    BandStartBPs: [862x1 int32]
      BandEndBPs: [862x1 int32]
      BandLabels: {862x1 cell}
       GieStains: {862x1 cell}

Plot the entire chromosome ideogram for Homo sapiens.

chromosomeplot(hs_cytobands);
title('Human Karyogram')

Display the ideogram of only chromosome 7 for Homo sapiens by right-clicking chromosome 7 in the plot, then selecting Display in New Figure > Vertical.
Plot the ideogram of only chromosome 15 for Homo sapiens in a horizontal orientation. Set the units used in the data tip to kilo base pairs.
```
chromosomeplot(hs_cytobands, 15, 'Orientation', 2, 'Unit', 2);
```
View a data tip with information about the chromosome by hovering the cursor over the chromosome. View a data tip with detailed information about a specific band by clicking the Data Cursor button on the toolbar, then clicking the band in the plot. To delete this data tip, right-click it, then select Delete Current Datatip.

Tip You can change the orientation of a single chromosome ideogram by right-clicking, selecting Display > Vertical or Horizontal. You can show or hide the band labels of a single chromosome ideogram by right-clicking, then selecting Show G-band Labels or Hide G-band Labels.

Adding a Chromosome Ideogram to a Plot

Load a MAT-file, included with the Bioinformatics Toolbox software, which contains coriell_data, a structure of CGH data.
```
load coriell_baccgh
```
Use the cghcbs function to analyze chromosome 10 of sample 3 (GM05296) of the CGH data and return copy number variance (CNV) data in a structure, S. Plot the segment means over the original data for only chromosome 10 of sample 3.
```
S = cghcbs(coriell_data,'sampleindex',3,'chromosome',10,...
           'showplot',10);
```
Use the chromosomeplot function with the 'addtoplot' property to add the ideogram of chromosome 10 for Homo sapiens to the plot. Because the plot of the CNV data from the Coriell cell line study is in kb units, use the 'Unit' property to convert the ideogram data to kb units.
```
chromosomeplot('hs_cytoBand.txt', 10, 'addtoplot', gca,...
               'Unit', 2)
```

Tip Before printing the above figure containing an added chromosome ideogram, change the background to white by issuing the following command:

set(gcf,'color','w')

Displaying Copy Number Alteration Regions Aligned to a Chromosome Ideogram

Create a structure containing segment gain and loss information for chromosomes 10, 11, and X from sample 3 from the Coriell cell line study, making sure the segment data is in bp units. (You can determine copy number variance (CNV) information by exploring S, the structure of segments returned by the cghcbs function in step 2 in Adding a Chromosome Ideogram to a Plot.) For the 'CNVType' field, use 1 to indicate a loss and 2 to indicate a gain.
```
cnvStruct = struct('Chromosome', char({'10', '11', 'X'}),...
                    'CNVType', [2 1 2],...
                    'Start', [66905000 25416000 1],...
                    'End',   [110412000 39389000 154913755]);
```
Pass the structure to the chromosomeplot function using the 'CNV' property to display the copy number gains (green) and losses (red) aligned to the human chromosome ideogram.
```
chromosomeplot('hs_cytoBand.txt', 'cnv', cnvStruct);
```

The coriell_baccgh.mat file used in this example contains data from Snijders et al., 2001.

References