JLGraph Online Page
Begin by bookmarking this page for future reference. Next, read the guide below on the required input file format. Once ready, select the location of your input file(s) and submit the query.
If you receive a "bad data" message, please check that you've entered valid names for the labels, and that your input file(s) conform to the CSV format described in the file format description page.
If you encounter any problems, or have any suggestions please email the author at kcarter@cyllene.uwa.edu.au.
JLGraph Input File Format
JLGraph accepts input data to be in the form of a CSV, or comma-seperated-value, file. Nearly all spreadsheet programs will export (save) CSV files directly. As many people work in Microsoft Excel, here's a guide how to save a CSV file from Excel.
Each input should consist of 3 or 4 columns of data.
The first column of the input file must contain the chromosome number eg 1,2,10,22.
The second column of the input file must contain the data to be plotted eg 2.4, 0.004.
The third column of the input file must contain the marker position. This can either be a distance figure (ie c position for each marker) or simply a marker number for the particular chromosome (sequentially ordered). Eg. 5 markers for chromosome 1, 3 markers for chromosome 2. Positions can 0,0.3,0.5,0.8,1.2 and 0,0.4,0.6,1.2 (c) OR 1,2,3,4,5 and 1,2,3 (marker num).
The fourth column is optional. This is used specifically when you are working with p-values and you wish to highlight those values considered "significant". If column 4 has p-values (column 2 can contains the same p-values) then significant values will be highlighted using the following:
p < 0.05 - a small circle is drawn above the marker to highlight the position
p < 0.01 - a small square is drawn above the marker to highlight the position
p < 0.001 - a small triangle is drawn above the marker to highlight the position
In the example to the right, we are using 2 chromosomes (in S Excel). Column A has the chromosome number (up to 22 can be plotted on a single page); Column B has the data to be plotted - in this case -log10 p value; Column C has the position of markers by centimorgan; Column D has the acutal p-values (used to highlight significant markers).
Just "Save as" and select "Comma Separated Value" to save your data as a CSV file. Feel free to play with the above sample CSV file.
Here's what this data looks like plotted in JLGraph (cross section of the pdf file generated). You might also like to see the actual PDF file generated from the above sample CSV file.
JLGraph Input Parameters Help
X-axis label. This is the label given to the X-axis - the distance between data points.
Y-axis label. This is the label given to the Y-axis - actual data to be plotted.
Dataset1 label. This is the label given to the data contained in the first input file supplied. This name appears in the 'Legend' for the jlgraph output.
Dataset2 label (optional). This is the label given to the data contained in the second input file supplied. This name appears in the 'Legend' for the jlgraph output.
Minimum y-axis value. This is the minimum value you would like to be displayed for the dataset(s) provided. If you find that data is not being plotted correctly, ensure that this minimum figure is smaller than data in the datasets provided.
Maximum y-axis value. This is the maximum value you would like to be displayed for the dataset(s) provided. If you find that data is not being plotted correctly, ensure that this maximum figure is larger than data in the datasets provided.
Graph title. This is the title displayed at the bottom of the jlgraph output page.
Graph orientation. JLGraph output can be either a single page portrait or single page landscape paper format.
Use lines to join data points? Select whether plotted data points should be joined by a spline curve. Convention suggests that when graphing linkage results, lines should be used, while plotting association (for example) results lines should not be used.
Use coloured lines? Select whether to display data point/lines in colour or in black and white.
Output as pdf/eps? Select whether to create the jlgraph output as a portable document file (pdf) , eg use Acrobat to view, or as an encapsulated postscript file (eps), eg use GhostView to view.
Show all / zoom a single chromosome? Select whether to display all chromosomes (up to 22) on a single jlgraph output page, or select a chromosome to zoom (expand) to take up the entire output page. Please note: output for any zoomed chromosome will always be in landscape paper format. You should select a chromosome number that exists within your dataset.
Referencing JLGraph
If you find this tool useful, or use any graphics produced in publications, please refer to:
Carter KW, Palmer LJ. (2004) JLGraph: Java Linkage Graph [ONLINE]
