MapChart ©
Roeland E. Voorrips, 1999 - 2023
Copyright notice
Disclaimer
FAQ (Frequently Asked Questions)
Version
How to refer to MapChart
What is MapChart ?
Installation
New features and upgrade issues
Upgrading from version 1.x
Upgrading from version 2.0
Upgrading from version 2.1
Upgrading from version 2.2
Drawing charts
Files and directories
Linkage groups versus Chromosomes
Marker distribution analysis
Data format
Linkage group header
Loci section
Segments section
QTLs section
Graphs section
Graph files
Chart options
Page size page
Title&Footer page
Page layout page
Colors&Lines page
Bars page
Loci page
QTLs&Graphs page
Homologs pages
Menu structure and Keys
File menu
Edit menu
Chart menu
Tools menu
Window menu
Help menu
Toolbar
Examples
Problems and solutions
Support
Index
The copyright to MapChart belongs to Wageningen University and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands. To obtain the software and a free personal license visit the MapChart pages at https://www.wur.nl/en/show/Mapchart.htm. For permission to distribute MapChart on a commercial or non-commercial basis please contact us through the contact persons listed on those pages.
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.
FAQ (Frequently Asked Questions)
This Manual is the final documentation for MapChart. However some questions that are frequently asked are addressed in a MapChart FAQ document which, like this Manual, is located in the MapChart program folder.
The current version is MapChart 2.32, released November 2017. The most recent version can always be found on the website of Wageningen University and Research (at the time of writing: https://www.wur.nl/en/show/Mapchart.htm).
A description of MapChart appears in the following publication:
Voorrips, R.E., 2002. MapChart: Software for the graphical presentation of
linkage maps and QTLs. The Journal of Heredity 93 (1): 77-78.
MapChart is a computer package that produces charts of genetic linkage and QTL data. These charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files. This information has to be calculated beforehand, usually with genetic mapping software such as JoinMap® and MapQTL®.
The charting needs of geneticists vary widely. Therefore MapChart comes with many options to adapt the charts to different purposes. However, no charting package can cater for all situations. Charts will often have to be adapted manually. Therefore MapChart is designed to produce graphic files which can be imported by and edited with other software.
MapChart will usually be installed through a setup program. This will create a new directory "MapChart", by default under the Program files (x86) directory. In this directory MapChart.exe, MCManual.htm (this manual) and several other files are placed along with a subdirectory "Examples". The setup program will also create a MapChart entry in the Start menu.
New features and upgrade issues
For an overview of the new features, enhancements and bug fixes since previous versions of MapChart, see the MCWhatsNew.htm file in the MapChart program directory. MapChart 2.0 was a completely rewritten version with many new features and a new user interface. Version 2.1 added the possibility to show homologies between loci on different linkage groups, Chart titles, the automatic vertical alignment of linkage groups to show that they belong to the same chromosome, and page footers with page number, date and/or file name. The main changes in version 2.2 were the "omit" option for locus names, the possibility to export bitmaps (*.bmp) as well as metafiles, and an extended graph file format that allows files to contain data for multiple linkage groups and the reading of MapQTL 5.0 output files.
Version 2.3 added more flexible zooming of the charts and had a more robust import of MapQTL 5.0 / 6.0 output files (the previous version was limited to only a few population types). QTL names can now be suppressed. Also a different installer was used as the previous one occasionally gave problems under Windows 7 and 8.
The current version (2.32) addresses an issue where on some systems MapChart could not create a window, a problem that sometimes arose or disappeared after a Windows update.
The current version of MapChart will import the *.map / *.set file pairs produced by version 1.x. All the old formatting is still valid, with the exception of the color codes. In version 1.x, the default color code was C0, and only codes C0 - C9 were available. The background color was specified separately and did not correspond to a color code. In contrast, the current version can handle up to 1000 color codes, code C0 specifies the background color and C1 the default color. When importing version 1.x files, MapChart automatically assigns the old background color to C0, and C0 - C9 to the new codes C1 - C10. In this way the charts are produced with the same colors as before. However, when editing these charts the new color codes must be used. Further, in version 1.x color codes could be specified with only the number; in the current version the number must be preceded with a "c" or "C".
In version 1.x, the command-line parameter /d=<default directory> could be specified with or without the "/" in front. The current version requires the "/", because the first parameter without "/" is interpreted as a file to be opened. It may therefore be necessary to change any shortcuts referring to MapChart.
Files of version 2.0 are generally displayed unchanged in version 2.3, with two exceptions:
In some cases small changes in the data are needed:
No changes are needed, all existing projects will still produce identical results.
In general, files produced by newer versions may be read incorrectly or not at all by older versions.
A map window in MapChart has two pages, which can be selected by clicking their tabs: the Data page, which shows an editor where the names, positions and formatting of the map elements are entered, and the Chart page where the charts are displayed.
The drawing of a chart starts with a linkage map, such as produced by JoinMap, with a sequence of linkage groups each with the loci listed in ascending order of position (Example 1). To each linkage group QTL bars and graphs can be added, and segments of the linkage groups can be highlighted. All this information is entered in the Data page (see Data Format), which is displayed when you choose File New from the Main menu. Map files can also be imported, by choosing File Open and selecting file type "Map file" (or "All files", if your map file has an extension other than ".map"); in that case the Chart page with the calculated chart is shown.
Chart Options (Tools menu) is used to specify the general appearance of the charts, such as the fonts used for the different elements, the various colors, the size and layout of the pages etc. Finally, for individual elements exceptions to these general chart option can be specified in the Data page, such as a different font size for specific loci, and extra formatting such as fill style, color codes can be added (see Data Format).
The chart pages are displayed by choosing the Chart tab, or by opening a map or MapChart data file. If no charts can be calculated because of errors in the data, or because the charts cannot be fitted on the page, an error message is shown and the Data page is displayed. After editing the data, select the Chart page to see the charts. Some common errors and solutions are discussed in the Problems section.
Once the charts are drawn, the Chart page opens showing the full page as it would appear on paper, including the margins. Menu commands, buttons and key commands are then available for navigating through the pages, moving around on the current page and zooming in or out (see Chart menu).
The data can be saved and printed by selecting File Save or File Print data from the Main menu. Chart pages can printed (Chart Print), or copied or exported as Enhanced Metafiles (Chart Copy or Chart Export). See the Problems section for solutions to some common problems with importing charts into word processing and presentation software.
MapChart datafiles have the extension *.mct. In addition, MapChart can read the *.map / *.set file pairs produced by MapChart version 1.x; on reading these files the color codes (that followed a different scheme in version 1.x) will be updated automatically. If a *.map file without corresponding *.set file is opened (such as map files exported by Joinmap) the Default Chart Options will be used. If a chart contains graphs, for each graph line the specified graph file must exist.
The Open file and Save file dialogs start in the last used working directory. If this directory is not accessible a default working directory will be used. This default directory can be specified with the command-line option /D=<dir>. If no default directory is specified, c:\ will be used.
MapChart can export chart files, each containing a page with one or more linkage group charts, in the same directory as the *.mct file. These chart files have the name of the *.mct file followed by a three-digit page number, and extension ".emf", indicating that they are in "Enhanced Metafile" format, or ".bmp" for Bitmap format. For example, exporting metafiles from a project named apple.mct will produce apple001.emf, apple002.emf and so on. These files can be imported into other applications such as word processors and presentation software. Please note that exported Bitmaps will generally be very large; in the order of 50-60 MB for an A4 page at a resolution of 600 dpi. Almost always Metafiles will be preferable to Bitmaps.
Also individual pages can be copied to the Clipboard (select Chart menu Copy page or the Copy Page button) and pasted into other applications that can handle enhanced metafiles. It may be necessary to use "Paste special" or "Paste as metafile" instead of "Paste" in the receiving application. See the Problems section for solutions to some common problems with importing charts into word processing and presentation software.
Linkage groups versus Chromosomes
In general, MapChart draws all linkage groups side-by-side as independent units. Linkage group declarations can start with the keywords "Group" or "Chrom"; they have exactly the same effect, and the "Chrom" keyword is only included for compatibility with older JoinMap versions.
However, sometimes it is known that two or more linkage groups represent different parts of the same chromosome. In this case it is customary to draw these linkage groups aligned vertically, one above the other. MapChart offers a possibility to do that, using the Align vertically parameter in the linkage group header. This parameter creates an aligned group of linkage groups, which are treated as a unit. This affects not only the drawing of the maps, but also the drawing of Homologs: Homologs between linkage groups within the same "aligned group" are drawn like homologs within the same linkage group. Also the Combine Maps tool treats these aligned groups as units.
If the Split Map chart option is active, the maps of long linkage groups are divided into parts that are drawn side-by-side. In that case, vertical alignment becomes pointless and the Align vertically parameter is ignored.
MapChart can help to study the distribution of different marker categories over the map. This can be useful for selecting e.g. AFLP primer combinations that together provide a good map coverage. There are two possibilities to do so:
MapChart reads linkage and QTL data from text files. These files must contain "flat text", such as produced by a text editor. MapChart cannot read text files in word processor formats. The text is displayed in an editor, which can be used to enter, inspect and modify the data.
The text containing the map data specifies a sequence of linkage groups. Each linkage group specification consists of a header line, followed by a loci section and optionally a QTLs, Graphs and/or a Segments section. Blank lines and lines containing only comments (i.e. lines where the first non-blank character is ";") may occur anywhere in the file and are ignored. Comments may also appear behind other information on a line: in that case the ";" must be preceded by blanks.
It is possible to let MapChart ignore loci or whole linkage groups
temporarily by "commenting out" the relevant lines.
In order to do so, place the ";" character at the start of all
relevant lines; by removing this character the information is made available
again.
The editor provides two
functions to quickly "comment" and "uncomment"
a whole selection of lines (choose Edit Comment lines or
Edit Uncomment lines from the main menu).
Many parameters for controlling different aspects of the chart elements are discussed below. An overview of these codes is available in the file "MapChart formatting codes.rtf" in the MapChart program directory. This file can be read and printed by any word processor.
The specification of a linkage group starts with the linkage group header. The header line of a linkage group starts with the keyword "group" or "chrom" followed by the linkage group name. The name will be shown with upper and lower case characters as entered. If the name contains blanks it must be enclosed by double quotes. If no name is desired, enter "" (two consecutive double quotes) if any of the other options are used.
After the name the following optional parameters may be supplied, in any order but all on the same line:
The names and positions of the loci (or markers) in the linkage group are specified in the Loci section. The loci section starts on the first line after the linkage group header, and continues until the start of the Segments, QTLs or Graphs section or until the next linkage group header. Each locus is defined on one line, which contains the following elements in this order:
The font and color information affects only the locus name and optional text, not the position or interval length numbers. The default color is the linkage group color (C1 if not set in the linkage group header).
Segments of the linkage group bar can be shown highlighted, with a special color or fill style (Example3 - homolog matching). These segments are specified in the Segments section. The Segments section starts with a line beginning with the keyword "Segments"; the rest of this line is ignored. The Segments section continues until the start of the QTLs or the Graphs section or until the next linkage group header. Each segment is defined on one line, which contains the following elements in this order:
The order in which the segments are defined is not relevant. Also the start and end of a segment may be reversed. The fill style of the linkage group (defined in the linkage group header) should be F0 (default, empty bar), and segments should not overlap, otherwise the printed result may differ from the screen display.
Along the linkage group map, bars can be drawn that show the extent of QTL support intervals. These QTL bars are specified in the QTLs section. The QTLs section starts with a line beginning with the keyword "QTLs"; the rest of this line is ignored. The QTLs section continues until the start of the Segments or Graphs section or until the next linkage group header. Each QTL is defined on one line. QTLs can be specified in two ways: as fully specified QTLs or as Auto QTLs.
Auto QTLs are derived from a graph (see next section and Example6 - auto-QTLs) with exactly the same name. An Auto QTL is located around the graph maximum, with the inner and outer intervals extending to the positions where the graph falls below the maximum minus the "inner threshold" and the "outer threshold" respectively.
A line specifying an Auto QTL is composed of the following elements:
The order in which the QTLs are specified is important. If a QTL fits behind the previous QTL (i.e. it starts at a higher map position than the previous QTL ends, and the names do not overlap), then they are placed in the same "QTL band": a vertical column of QTLs. Otherwise a new QTL band is started, one step further from the linkage group bar (Example4 - QTLs and split map).
On the right side of the linkage group map, graphs can be drawn that show how some parameter (e.g. a QTL LOD value) varies along the map (Example6 - auto-QTLs). These graphs are specified in the Graphs section. The Graphs section starts with a line beginning with the keyword "Graphs". The rest of this line is used to specify the Y-axis formatting and can contain the following elements:
The Graphs section continues until the start of the QTLs or Segments section or until the next linkage group header. Each line in the Graphs section specifies either a constant (a line with constant Y value over the length of the linkage group) or a graph.
A graph is defined on one line, which contains the following elements in this order:
A constant (e.g. indicating a LOD threshold value) is similarly defined on one line, as follows:
The keywords ("group", "chrom", "segments", "QTLs", "graphs", "auto", "const") and the formatting information can be entered in upper or lower case. All names, texts etc. are shown with upper and lower case characters as entered.
Examples of MapChart files showing and explaining all these options are installed in the MapChart\Examples directory.
Graph files contain the coordinates of all the points specifying graph lines. From version 2.2 the format of graph files has been extended to allow data for multiple linkage groups to be specified in the same file, which should reduce the clutter of files.
A Graph file starts with a line of column titles; subsequent lines contain the values for a series of points (in order of increasing map position, and grouped per linkage group). MapChart uses the value in column "cM", "map" or "position" as the map position of the point, and by default the value in the column "lod" as the function value. If present, the column "group" lists the linkage groups; this is needed in files containing data for multiple linkage groups. If a value (or any text) is present in the last column, a symbol is shown at that point in the graph. Instead of the "lod" column, any other column title may be specified for the function value, using the T=<column title> formatting option of the graph. In this way, one graph file can define multiple graphs, each specified using a different column title. Using the comment character (";"), comments may be added at the end of a line or between lines.
The keywords "cM", "map", "position" and "group", and the column name for reading the Y-values are not case-sensitive. In contrast, the name of the linkage group listed in the "group" column must be exactly identical to the name of the linkage group in the MapChart file. If the group names in the Graph file are different from those in the MapChart file, the G=<groupname> option can be used to specify which group name to read from the graph file.
Graphs may contain points with map positions beyond the linkage group start or end, but only the part between the linkage group start and end will be shown. Points with function values outside the specified Low or High ends of the Y-axis will cause the Y-axis range to be extended. Further, if the file does not contain a "group" column, or if only one group name occurs in this column (even if different from the linkage group where this graph belongs), all the lines of the file are read.
For compatibility with earlier MapChart versions, the line of column titles may be omitted. In that case the first column should contain the map positions, the second column the function values, and if a third number or text is present on a line a symbol will be shown at that point. Such files define a graph for a single linkage group.
MapChart can read the output of MapQTL 3.0 and 4.0, as exported using the "Copy text" command, and the output of MapQTL 5.0 and 6.0 as exported using the "Export to File" command. By default, MapChart will use the "LOD" column for function values in the case of Interval mapping or MQM mapping, and the "K*" column in the case of Kruskal-Wallis analysis. Dont edit the MapQTL files, e.g. by adding lines, columns or comments, else the format may not be recognized.
The "Chart options" item on the Tools menu or toolbar displays the Chart options form, which is divided into several pages: Page size, Title&Footer, Page layout, Colors&Lines, Bars, Loci, QTLs&Graphs and Homologs.
MapChart produces output in the form of one or more pages. In the region inside the margins a chart title may be shown at the top. Below the chart title, one or more linkage group maps are drawn side by side. The printed output consists of the pages with the specified margins; the produced metafiles (and the page images copied to the Clipboard) only contain the rectangular region containing the charts, excluding the page margins. Use the Page size tab to specify the paper size and orientation, and the page margins.
Optionally, a chart title and a footer can be shown on the pages. On the Chart options - Title&Footer tab, the following options can be set.
In the area between the title and the footer the linkage group maps are shown side by side. Directly below the chart title is a region where the names of all linkage groups appear, and below that is the "Chart area". The Chart area contains the linkage group bars and all surrounding objects such as the loci, QTL bars and graphs.
On the Chart options - Page layout tab, the following options can be set.
In MapChart a color palette is used to specify the colors of the different chart elements. On this page the number of colors in the palette is set, and the actual colors used for each color code are defined. Codes C0 to C10 are pre-defined, but these can be deleted (except codes 0 and 1), changed, or extra color codes can be defined. It is possible to define a large number of extra color codes, which initially all get the same color value (see Add range). This may be useful when dealing with many categories of loci (e.g. AFLP markers based on many different primer combinations): assign each category its own color code, but assign the same color value to all these codes. To highlight the loci of one particular category, just change the color value of its color code (Example5 - marker highlighting and footer).
Also on this page the width of normal and wide (bold) lines can be set. Note that these will be approximations: depending on the resolution of your printer usually the specified line widths will be equivalent to only few pixels. Most lines in the charts are "normal"; some line can be specified as wide, including indicators of highlighted loci, QTLs, graph lines and connections between homologs.
Default widths are 0.2 and 0.5 mm for normal and wide lines respectively; maximum values are 1 and 2 mm; wide lines must be at least as wide as normal lines. All lines will be at least one pixel wide.
QTL options:
Graph options:
MapChart can highlight homologies between loci. Loci can be grouped into homologs groups based on similarity of their names, and/or based on their homolog number which can be specified on the Data sheet. Each locus can be part of only one homologs group. Loci in the same group are shown in the same color and connected by lines, if these options are selected.
If the "Match locus names" checkbox (see below) is NOT checked, loci with the same homolog number are grouped together. If the "Match locus names" checkbox is checked, the loci are grouped in the first place based on name similarity. Further, loci that you wish to remove from such a group you can give a NEGATIVE homolog number (if you give several loci the same negative homolog number, they will form a new group). If you want to add extra loci to a group, give the same POSITIVE homolog number to those loci and to one or more of the loci already in the group.
The Combine Maps tool makes it easy to place corresponding linkage groups from different files side by side, so that homologies can be clearly shown.
The options on these pages specify how to show homologs:
The OK button will accept the new chart options, the Cancel button reverts to the old chart options. Further the "Defaults" button will open the default chart options dialog. Here the current chart options can be saved as defaults: this means that they will be applied to new files and to imported map files. Also, the current chart options can be replaced by the previously saved default options or by the original (pre-set) chart options. The chart title will not be saved or replaced in these cases.
The main Menu has the following submenus: File menu, Edit menu, Chart menu, Tools menu, Window menu and Help menu.
The Edit menu is only available when the Data page of the current map is showing.
The Chart menu is only available when the Chart page of the current map is showing.
Additionally the following key combinations are available for moving around the current chart page: arrow keys for small jumps, Ctrl-arrow keys for large jumps, Home to left side, End to right side, Ctrl-Home to top-left corner, Ctrl-End to bottom-right corner.
Chart options
Use this menu item, the Chart options button or Ctrl-T to open the Chart options dialog
Use default options
Replace all current options by their default values, if defaults have been set previously, and else by their original (built-in) values.
Use original options
Replace all current options by their original (built-in) values.
Set default options ...
Save the current chart options as default options in a file named MapChart.mct. These options will be used for new maps and can also be applied to existing MapChart projects using the Tools menu item Use default options.
A facility to update a newly imported map with formatting from a
previous map. Useful when a map has been recalculated or new loci
have been added, and you want to apply the formatting of a previous
version of the map to the new map. When selecting this command,
the target map (the new map which must receive the formatting) must
be the active map, and the source map (the older version, where the
formatting must come from) must also be open. Use the dialog to specify
which map is the source map, and which items to copy from the source map:
Linkage group: copy from the source linkage group
with the same name the formatting, comment, QTLs, Graphs and
Bar segments; the last three items only if they are not present in
the target linkage group.
Loci: copy from the locus with the same name the
formatting and comment. If the locus in the source map is present
in the same linkage group (with the same name), then that locus is
used as source; else the source map is searched from the start for
the first locus with the same name.
Chart options: copy all the Chart options, including or
excluding the chart title of the source map.
This tool takes two or more open map files and produces a new map
with first all the first linkage groups of the original maps,
then all the second groups etc.
Useful to compare maps and show homologies
between maps, or to combine separate maternal and paternal maps.
Use to recalculate the charts when the graph files have been changed. After changes in the map data on the Data page, the charts are recalculated automatically.
If the charts dont fit on the page, use the Autofit utility to search for a suitable new combination of Chart options. Autofit is automatically used the first time the charts are drawn (the first drawing of a New map, or the first drawing after opening a file) if the current Chart options don't allow the chart to be drawn. Autofit will only check out the Chart options; if the problem is caused by formatting of the data (e.g. a too large vertical shift of the linkage group bars) then Autofit wont be able to solve this.
Use the Data Font dialog to set the font used on the Data page.
MapChart can open multiple maps at the same time; use the Window menu to select and arrange the maps
For the function of the tool bar buttons, see the "ToolTips" that appear when you position the mouse pointer on them and the description of the equivalent Menu items.
Two buttons change function depending whether the Data page or the Chart page of the current map is showing: the Print button (print data or chart pages) and the Copy button (idem). Several other buttons are disabled either with the Chart page or the Data page showing.
The Zoom field allows to scroll to the desired zoom level. It is also possible to enter the zoom level directly; any level from 10% to 1000% is allowed, as are f (full page view) and p (print resolution)
Several examples are provided in the MapChart\Examples subdirectory. These are MapChart files (*.mct) showing the use of many parameters and chart options. Before opening these files you may want to make a backup, so that you can go back to the original files without re-installing MapChart.
On opening the example files, MapChart will show the chart pages. Select the Data tab to see the data. In the Data sheet, you will also see explanations of the use of the parameters, and suggestions to try out different chart options and parameters. The following examples are provided:
Example1 - basic map:
Basic map data of two linkage groups, without any formatting or QTLs.
Example2 - formatting:
Map with two linkage groups, showing many linkage group header and locus options, including the vertical aligning of linkage groups.
Example3 - homolog matching:
Map showing four homologous linkage groups, with homologous loci and homologous bar segments highlighted.
Example4 - QTLs and split map:
Map showing two linkage groups, each with several QTL intervals, some overlapping. This example also shows the effect of splitting up the map into segments.
Example5 - marker highlighting and footer:
In this map, every category of markers has its own color code. By setting all color codes to black and one to red, it is easy to study the distribution of the different marker categories over the genome. Also shows effect of formatting code o ("omitted") for loci.
Also the effect of showing page numbers in the chart title is demonstrated.
Example6 - auto-QTLs:
Map with two linkage groups, each with one QTL. The QTLs are shown in three ways: (a) the significance of the Kruskal-Wallis test at each locus is indicated by asterisks in a separate text column, (b) the LOD graphs along the linkage groups are shown, together with a constant line indicating the LOD threshold, and (c) 1- and 2-LOD intervals are shown, calculated automatically from the LOD graphs.
Example7 - multi-QTL and graphs:
Here, 3 LOD graphs and 3 auto-QTL intervals are shown on the same chromosome.
No map data available: This error message will appear if MapChart cannot find the start of the data. The data should start with the heading for the first linkage group (starting with the word "group" or "chrom"). If you have other text appearing above the first linkage group, delete it or comment it out (place a semicolon at the start of each comment line).
Error in position of locus: MapChart expects a valid number after the marker name, indicating the position; the loci must be listed in order of ascending position.
Error in point in graph : Each line in a graph file should give at least two valid numbers (see Graph files). The points must be in ascending order of X (map position) values.
Error messages stating that the charts dont fit in the available
space: Probably the height of the charts is larger than the space
between the page margins. This can be solved by increasing the available
page height, and by decreasing the chart height.
The page height can be increased by choosing a portrait instead of
landscape paper orientation and by setting smaller margins
(both through the File Chart page setup menu option).
The chart height can be decreased by changing several chart options
(Tools - Chart options menu option or toolbar button).
Most effective will be choosing a smaller Locus font size,
increasing the number of locus names per line
(both on the Chart options Loci page), and splitting linkage groups
into segments ("Split map interval" in the
Chart options Bars page). Also choosing a smaller Title, Name or
Y-axis font may help.
Finally shifting linkage group bars up or down may cause them to move
outside the chart area; in that case their length must be decreased,
or the shifting must be adjusted. The Autofit
utility can check out many of these combinations.
Changes in graph files dont appear in the charts: When MapChart needs to display a chart, it first checks if there are changes on the Data page or in the chart options. If not, no new charts are calculated and the previously calculated charts are shown again. Since changing a graph file does not change the Data page, the charts will not be recalculated. In this case select Recalculate from the Tools menu or button bar: this causes the data and graph files to be read again and new charts to be calculated. Also make sure that you have saved the edited graph file before recalculating the charts!
Charts imported into other applications are printed with very thick lines: When MapChart draws the charts, the width of lines is as specified on the Chart options - Colors&Lines tab, but at least one pixel of the output device. If no Windows printer is installed, the screen resolution will be used, which is very coarse, so even one pixel may appear quite thick. Try generating the charts on a computer with a printer, and the charts will be drawn using the printer resolution. The same problem occurs when the computer is running in "Safe Mode": in that case no printer drivers are installed.
Some chart elements appear distorted after importing into MS-Word or MS-PowerPoint: To avoid changes on importing, make sure that the imported image does not have to be resized. Images exported from MapChart (either by saving as *.emf file, or by copying to the clipboard) contain the area within the margins; by a suitable combination of page and margin sizes (Chart options - Page setup) the desired size can be obtained. Also, exporting the *.emf file from MapChart and importing (Insert Picture from file) seems to give better results than copying via the Clipboard.
Texts and names in charts imported into other applications are not drawn at the correct size: When charts are only imported into word processing or presentation software there is no problem. However, when the charts are edited (especially if they are "split into objects" or "ungrouped") they may be converted to the internal format of the importing application. At that moment, fonts may change a little in size, causing texts to become somewhat wider and to overlap if they are positioned close together. For example, this happens in Microsoft PowerPoint when the "Ungroup" command is used. This is usually almost invisible when charts are drawn at the printer resolution, but can be problematic when drawn at screen resolution (on a computer with no printer installed). It also depends on the font and font size used. If the problem arises, try generating the charts on a computer with an installed printer, and/or try changing fonts or font sizes.
Charts copied to MS PowerPoint are shown very small: If charts are copied to MS PowerPoint through the Clipboard (using the Copy Page button or Ctrl-C), they must be pasted using Edit Paste Special Enhanced Metafile in MS PowerPoint. Using the Paste button or Ctrl-V results in a very small picture. Another way to import charts into MS PowerPoint is Insert Picture From file, after using Chart export in MapChart.
Graph lines in charts imported into other applications cannot be edited: The dashed and dotted lines in graphs are composed of short line segments. After importing a chart into another application and "splitting to objects" or "ungrouping", the graph lines are not one object any more, and cannot be edited as a whole. The solution is to draw with solid lines (line style L1, the default value) in MapChart; solid lines remain one object after imported charts are split. In the importing application the line style can then be changed as desired.
White lines and texts are invisible: If you need white graphics on a transparent background, e.g. to place them on a dark background in another application, choose a dark color for the background (color code C0) in the Chart options - Colors&Lines page dialog, and check "Background transparent". In MapChart you will see the charts against a dark background, but the copied or exported metafiles will have a transparent background.
Questions, problems, bug reports and suggestions for improvements and
additions can be sent to the author at
roeland.voorrips@wur.nl.
In case of problems, send the file(s) together with a description
of the problem.
The most recent version can always be found on the MapChart pages at
https://www.wur.nl/en/show/Mapchart.htm.
Add color range
Align linkage groups side by side
Align linkage groups vertically
Auto QTLs
Autofit
Bar options
Bar segments data format
Bold (wide) lines
Chart files
Chart options
Chart page
Chart title
Chromosomes and linkage groups
Citation
Color codes, defining
Color codes, Upgrade issue
Combine maps
Comment lines command
Compare maps
Connections between homologous loci
Cursor keys
Data font
Data format
Data page
Default Chart options
Default directory
Default directory, Upgrade issue
Distribution of marker categories
Emf files
Examples
Exporting charts
FAQ (Frequently Asked Questions)
Fill styles: select Help Fill styles
Footer
Format, data
Format, graph files
Graphs data format
Graphs - options
Graphs - legend options
Graphs - Y-axis data format
Graphs - Y-axis options
Homologous loci - Highlighting
Indicators - Highlighting and size
Keyboard commands
Legend options
License
Line styles: select Help Line styles
Line width
Linkage group - data format
Linkage group - bar options
Linkage group - bar segments data format
Linkage group - name options
Linkage groups - align horizontally
Linkage groups - align vertically
Linkage groups and Chromosomes
Loci data format
Loci - options
Locus texts
Map analysis
MapChart reference
MapQTL export Map file to
MapQTL read Graph files from
Margins
Marker (Graph symbol)
Markers: see Loci
Marker categories
Menu structure
Options - chart
Page setup
Print charts
Print data
QTLs - auto
QTLs - data format
QTLs - options
Recalculate
Referring to MapChart
Resolution
Segments data format
Split map
Symbol styles: select Help Symbol styles
Text columns
Title
Uncomment lines command
Update
Upgrade issues
Website
Wide (bold) lines
Y-axis of graphs - data format
Y-axis of graphs - options
Zoom field - button bar