MapChart FAQ (Frequently Asked Questions)

Introduction

MapChart is no longer actively developed or supported as its developer (Roeland Voorrips) has retired. However we have prepared this FAQ to answer most common questions. In addition there is a manual in html format in the MapChart program folder (usually c:\Program Files (x86)\MapChart\ or similar) that can also be accessed from the MapChart Help menu.

Also in the program folder several examples are provided. Take a minute to open these files: they may give you new ideas and show how to work with QTLs, LOD graphs, formatting and more.

Getting and installing Mapchart

MapChart can be found at https://www.wur.nl/en/show/mapchart.htm.

A Windows installer can be downloaded using the Download installer button. The download is a zip file that contains one file named MapChart232Install.exe. Unzip this file and execute it; it will install MapChart and create a link in the Start menu.

License and copyright

The copyright of MapChart belongs to Wageningen University and Research, Wageningen, the Netherlands. MapChart may be used for free by anyone and any organization, commercial or otherwise, but at one’s own risk. MapChart may not be distributed for commercial purposes otherwise than by sharing the download link(s) provided by Wageningen University and Research. Use in an educational or academic setting, including in classes and groups, is expressly allowed.
This software has been designed with care and is believed to perform as intended. However, neither Wageningen University and Research, nor any of its subsidiaries or employees accept any liability for material or immaterial damage resulting from the use of this software.

Is MapChart compatible with my OS or Windows version?

MapChart will run on any 32-bit or 64-bit Windows version, from Windows95 up to (at the time of writing) Windows11. MapChart is not available for Linux or Apple OS.

The map is too high to fit on the page, what can I do?

If the charts are too high to fit on the available space, a message to that effect will be shown or the chromosomes will be split into segments shown side by side. There are several things that can be done:

• Increase the available space
  The total height of the space available for the charts is determined by the page height, minus the top and bottom margins, minus the height of the chart title, minus the height of the Title bottom space (i.e. the space between title and linkage group names), minus the height of the linkage group names, minus the height of the Names bottom space (the space between the names and the chart area), minus the height of the footer.
  All these can be set in the Chart options dialog, tabs “Page size”, “Title&Footer” and “Page layout” (including portrait instead of landscape orientation).
  To make use of the increased space also increase the bar length.
• Decrease the height needed by the chart
  The height needed by the charts is the maximum of
  (1) the length of the longest chromosome bar and vertical shifts of chromosomes and
  (2) the space needed to print the locus names and positions.
  (1) is affected by "Bar length" on page “Bars” of the Chart options dialog and by vertical shift formatting specified for the individual linkage groups (indicated after the linkage group names in the chart data, see the MapChart manual).
  (2) is affected by the locus font size, number of locus names per line and the method for showing the positions; all on page “Loci” of the Chart options dialog:
  Increasing the number of locus names per line allows more locus names to be shown side-by-side instead of under each other, if they are at the same (rounded) position. The rounding of positions is determined by the Decimals specified on this page.
  Setting Locus names per line to 0 suppresses all locus names; when this is combined with Position methods “No positions” or “Ruler at page margin”, the loci cannot cause a chart height problem anymore.
  Instead of suppressing all locus names by setting Locus names per line to 0 it is also possible to show just some specific loci. Add formatting code “o” (for “omit” ) after all loci except the ones whose names should be shown. The “omitted” loci will still be shown as lines on the chromosome bar.
• Split linkage groups into segments
  By splitting linkage groups into segments of fixed size that are shown side by side a chart can be made to fit on the page. Set “Split map interval” on page “Bars” of the Chart options dialog to the desired length of the segments. Setting this to 0 removes the splitting.

Map units, mixing genetic and physical maps

Can I draw maps with basepair coordinates instead of cM (centiMorgans)?

Yes, in principle any type of unit can be used, but MapChart was designed with maps of a few tens to a few hundreds of cM in mind. Larger numbers may look ugly when positions are shown. Also if positions are shown as fixed tick intervals or using a ruler at the page margin the results may not look nice if very small or very large distances occur. These problems may be avoided:

• By not showing any position indicators
• By re-scaling the positions (e.g. using kB or MB units rather than base pairs)

Can I show genetic (cM) and physical (base pairs) maps side by side?

Yes, but MapChart uses only one units system for all maps. Therefore you need to re-scale the physical map positions so that their lengths are in the same numeric range as the genetic maps.

A different solution is to draw the physical and genetic maps in separate MapChart projects, each with their own scale, and to combine the two using e.g. PowerPoint. (MapChart exports images a.o. in emf format; if this is imported in PowerPoint the entire image can be “ungrouped” in successive steps and separate linkage group maps can be moved).

QTL bars

What is the difference between an “auto QTL” and a “normal” QTL?

In the case of a normal QTL the QTL bars are defined directly in the MapChart file:
after the QTL name 4 positions are given: the start of the outer (e.g. 2-LOD) interval, the starts of the inner (1-LOD) interval, the end of the inner, and the end of the outer interval, e.g.:
demo_qtl 50 60 70 80

The limits of an “auto QTL” bar are calculated from a LOD graph:
given the graph data (in a separate file, see below in the section on graphs) MapChart computes the extent of the inner and outer interval automatically based on the LOD-difference thresholds that are given in the auto QTL definition: 2 numbers after the QTL name and the “auto” keyword, usually 1 and 2 for the 1-LOD inner and 2-LOD outer interval, e.g.:
demo_qtl auto 1 2

I get an error message about a QTL

Some common errors are:

• the QTL name contains a space: enclose the name in "double quotes". Make sure that these are ordinary double quotes ("") and not the “pretty quotes” generated by e.g. Word (“”).
• The 4 positions of a “normal” QTL are not in ascending order
• The two thresholds of an “auto QTL” are not in ascending order
• An “auto QTL” refers to a graph that is not specified. A graph with exactly the same name must be specified in the Graphs section.

How can I show just one interval, not an inner and an outer interval?

The standard representation is an inner (1-LOD) interval as a rectangle, and the outer interval as lines extending from the inner interval and ending with whiskers. There are 3 possibilities to show a QTL as just one interval:

• Just a line with whiskers at the ends:
  give 3 times the start position and once the end position, e.g.:
  demo_qtl 50 50 50 70
• A line with whiskers at the end and an indicator of a point (say, the LOD maximum) within that interval:
  give the start, 2 times the max.LOD position, and the end position, e.g.:
  demo_qtl 50 60 60 70
• Just a rectangle like the inner interval, no outer interval:
  give 2x the start and 2x the end position, e.g.:
  demo_qtl 50 50 70 70

For an auto-QTL there are two options:

• A line with whiskers at the end and an indicator of the LOD maximum within that interval:
  give as LOD-difference thresholds 0 and the one defining the interval, e.g.:
  demo_qtl auto 0 2
• Just a rectangle like the inner interval, no outer interval:
  give 2x the same LOD-difference threshold, e.g.:
  demo_qtl auto 2 2

How can I show multiple QTLs on the same linkage group?

A linkage group can have only a single qtls section, but within that section (i.e. under the line that starts with “qtls”) you can define multiple qtls, each on a separate line.

Can I draw auto-QTL bars based on Kruskal-Wallis scores instead of LOD scores?

In principle you can calculate auto-QTLs based on any set of values, so also on e.g. the KW scores. However it is not meaningful to draw an auto-QTL based on the KW scores, as there is no fixed relation between the KW value and the probability of finding the causal gene in the interval, as is (approximately) the case for LOD values in Interval mapping.

LOD graphs

Is it possible to draw multiple LOD graphs alongside the same linkage group?

Yes, that is possible, but all graphs will be plotted in the same frame, using the same Y axis. A linkage group can have only a single graphs section, but within that section (i.e. under the line starting with “graphs”) you can define multiple graphs, each on a separate line.
One or more of these graphs can be constants: lines that indicate the (LOD) threshold over the entire linkage group. Examples 6 and 7 (located in the MapChart program folder) demonstrate this.

I have a file with LOD data but MapChart cannot open it

That is correct. MapChart can only open files in the joinmap / MapQTL map format, or its own *.mct MapChart project files. In order to import LOD data to draw a graph you need to define the linkage group in the normal way (i.e. start with a line for the group name, then the marker names and positions), and under that map definition start a graphs section with the keyword “graphs”. Then you can define graphs, each on one line, starting with the name, followed by the file from which to read the LOD data. A very short example (where mygraph is the name given to this graph, and MQout.dat the file with the LOD data):

group A
Mrk1 0
Mrk2 10
Mrk3 50
graphs
mygraph MQout.dat

For more examples see Examples 6 and 7 (located in the MapChart program folder).

I get an error message about a graph

Some common errors are:

• the graph name contains a space: enclose the name in "double quotes". Make sure that these are ordinary double quotes ("") and not the “pretty quotes” generated by e.g. Word (“”).
• The file name refers to a file that is not in the same folder as the MapChart project:
  it is possible to include a path in the file name, but probably it is easier to just copy the file to the folder with the MapChart project
• The file name contains spaces:
  enclose it in "double quotes" (again, not in Word’s “pretty quotes”).
• The file is not in the correct format:
  make sure it is either a file exported by MapQTL (up to version 6, at the time of writing) or it is in the format as explained in the MapChart manual.

Bar segments

How do I highlight a segment of the chromosome bar to show e.g. the centromeric region?

Below the map of the linkage group add a segments section using the keyword “segments”. Below that specify the segment as start and end position, followed by desired formatting. See “Segments section” in the manual.

Fitting maps on a page

My linkage groups are split into segments

When importing map data, MapChart attempts to fit the maps on the default page size, if needed by adjusting some of the chart options. As a last resort it will set the Split map interval option (on the Chart Options dialog, page Bars) to some value larger than 0. For example, if it is set to 50 the maps will be split every 50 cM. Set this option back to 0 to undo the splitting. Of course you will have to adjust other options then, see next question.

Other questions

How can I draw a decimal point instead of a decimal comma, or v.v.?

There is no option in MapChart to control this, it depends on the Windows settings. Probably you can change that in Regional settings of the Control panel or Settings app or something similar.

MapChart will read files with decimal points or decimal comma's, irrespective of the Windows settings: it first attempts to read the data file according to these settings and if that fails, it switches points and comma's in all text strings representing numbers and tries to interpret them again. There should be no thousands-separators in the numbers.

Note that there may be differences between the settings in Windows and in Microsoft Office on your computer; MapChart is sensitive to the Windows but not to the Office settings.