Kelviz is a graphing application designed to plot and annotate genetic data analysis results for easy review and publication. It is designed for use with Kelvin analysis results, but can make use of any data file that follows roughly the same conventions.
Kelviz works with a figure, which is created by importing output files from Kelvin analyses (or similarly-formatted data files), and consists of one or more plots, each of which may contain one or more lines (one per chromosome per genome), which are organized into line groups (by chromosome) and line sets (by genome). Line groups are displayed side-by-side in Kelviz plots, and multiple line sets can be added to overlap different genomes and/or different analyses. Plots can be laid out virtually anywhere in the figure, and may optionally use the lines from another plot so as to create different views of the same data. Gene marker maps can also be added, displayed as symbols overlaid on chromosome lines.
Kelviz works with figures in its own custom-designed XML file format, GRX, and can also export figures to several common raster and vector image formats such as PNG, TIFF, EPS, SVG, and PDF - either the whole figure at once, or in tabular collages of sub-plots per chromosome group or per line set.
See the v3.3.1 release notes for information as to what's changed with this version of Kelviz.
Kelviz is distributed as a Python source archive (both stand-alone and included with Kelvin), as a OSX app bundle, as a Linux shell script installer, and as a Windows .EXE installer.
The app bundle is tested on systems running Mac OSX 10.6, 10.7, and 10.8 (Snow Leopard, Lion, and Mountain Lion), and is the recommended means of using Kelviz.
The Linux installer and build is tested in commandline mode. The binary should hypothetically work anywhere, although this has not been broadly tested. Run the installer using bash Kelviz-3.3.1.install.sh and it will prompt you for a prefix to install Kelviz into.
The Windows installer and build is not extensively tested but is known to run on Windows XP SP3.
The source package can be used to build stand-alone apps for other platforms (setup files for pyinstaller and py2app/py2exe are provided), and it can also be used to simply run Kelviz directly from the distribution directory (see Running Kelviz, below). The following versions of Python and Python modules are required:
Nearly all these requirements are provided out-of-the-box by Continuum Analytics' Anaconda python distribution. wxPython 3 is not normally included in their default install (as of version 2.1), but can be easily added after installation by running conda install wxpython.
Kelviz can be run directly from the distribution directory by running:
$ ./kelviz.py
On OSX, simply double-click the app bundle to launch Kelviz via the Finder. On Linux, you can run kelviz (assuming that you installed it to a directory on your PATH) from any prompt. On Windows, you can find Kelviz in the Start menu after installation.
In all three cases, command-line options can be specified by running Kelviz from a command line; see that section for details.
Upon opening Kelviz, you can expect to see something like this:
The notable portions of this screen are indicated here:
You can have more than one Kelviz window open at the same time and thus work on figures side-by-side. To facilitate this, in the File menu you will find the option Open New Kelviz Window, which starts a new Kelviz window with a blank figure for you to start working on.
Loading an existing figure is done by clicking on the Open GRX File toolbar button (illustrated to the right), or by selecting Open GRX File from the File menu.
If you prefer to start working on a new or existing figure in place of the figure already loaded, you can do so by going to the Edit menu and selecting Clear Figure. Make sure you save any changes to your existing figure before doing this!
When you're at a stopping point (or want to make sure your work won't be lost), you can save your current work by clicking on the Save GRX File toolbar button (illustrated to the right) or by selecting Save GRX File from the File menu. Alternatively, if you don't want to overwrite a GRX file you started with, select Save as GRX File from the File menu and you will be prompted for a new filename.
Adding data to a figure - whether it be a plot from an existing figure, or the first data to be plotted in a figure, or another dataset to supplement what you already have - is done via importing that data into your figure. Data consists either of another Kelviz GRX file (for a figure with plots you want to import), or a Kelvin analysis or some other text file that follows the same conventions (for a dataset).
To import a plot from an existing figure, select Import Plot From GRX from the File menu. Enter the name of the GRX you wish to import a plot from. Kelviz will then ask you which plot to import with the following dialog:
Simply select the plot (or "All Plots" if you want to import them all) and they will be copied to your figure.
To import data with which to create a new plot, start by by clicking on the Import Data From File toolbar button (illustrated to the right) or selecting Import Data From File from the File menu. You will be prompted for a filename. Enter the name of the datafile you wish to import.
When doing this, Kelviz will need additional information as to how to import the data, and will prompt you for it via the following dialog:
The appearance and presentation of data in Kelviz can be modified after importing. This can be done on a per-lineset (per-genome), per-line (per-chromosome), or figure-wide basis.
The most common such operation is to change data presentation on a per-lineset basis, using the Configure Line Sets dialog. This is done by going to the Options menu and selecting Configure Line Sets.
Tabs are presented for each plot in your figure, and each such tab presents a row of controls for each lineset in that plot.
The "Use lines from another plot" controls are used to create plots with the same data as other plots - see Multiple Plots With The Same Data, below, for details.
NOTE: If you've customized any of the above properties for individual lines in this lineset, setting properties here WILL override those customizations!
Changing lines on a per-individual-line basis can be done via the Configure Individual Lines dialog, reached via the Options menu and selecting Configure Individual Lines.
Each and every individual line in the figure is represented, organized by plot and by chromosome. The controls are identical to those found in the Configure Line Sets dialog, above.
Alternatively, you may opt to change one or more properties of all lines at once. To do this, the Configure All Lines dialog (reached by going to the Options menu and selecting Configure All Lines) may be used:
The controls presented operate similarly to those in the Configure Line Sets dialog, except that they apply to each and every line in each and every plot in the figure. Each control also has a checkbox above it - if you do not want to change this property for every line, uncheck that property's checkbox to disable it. For example, if you want to change the line style of every line in the figure to "dotted" and leave everything else alone, uncheck the checkboxes under "Color", "Thickness", "Symbol", and "Symbol Size", change the "Line Style" drop-down to "dotted", and click OK.
Horizontal lines can be added to or removed from plots using the Add Or Remove Horizontal Lines toolbar button, illustrated to the right, or by going to the Edit menu and selecting Add Or Remove Horizontal Lines.
When adding horizontal lines, you will need to provide the Y-value or values where the horizontal line(s) should be located. Multiple horizontal lines can be added if desired; separate the values with commas.
You also have the option to set the width of horizontal lines for this plot; the value is specified in points.
Removing horizontal lines is done using the checklist at the bottom of the dialog that lists all horizontal lines in the plot by Y-value; put a check mark next to the horizontal lines you want removed and then click OK, and they will be removed.
The locations of plots relative to eachother in Kelviz is controlled via a conceptual "grid" of relatively-sized rows and columns. This layout system, plus details on the figure's size, can be adjusted via the Configure Figure Layout dialog, which can be reached by going to the Options menu and selecting Configure Figure Layout.
Several labels can and/or are automatically added to your plot to help clarify it, including but not limited to the chromosome numbers along the x-axis, additional x-axis and y-axis labels, and the figure title. These can be changed via the Figure Labels dialog, reached by going to the Options menu and selecting Configure Figure Labels.
The dialog is roughly divided into three parts - one for figure-wide options, and then one each for each plot's axes titles and x-axis chromosome numbers.
The following options are specific to each plot:
Each plot comes with its own legend, which is automatically generated and includes every visible line set. It is also possible to have a single legend for the entire figure, which includes information from every plot. To configure these, go to the Options menu and select Configure Figure Legends.
The following options are specific to each plot:
Tick marks along each plot's X-axis can be extensively customized. This is done via the Configure Tick Marks dialog, reached by going to the Options menu and selecting Configure Tick Marks.
There are three main choices for tick mark placement: Default, Base-Pair, and Custom.
1000 and setting "Add label to each tick mark" to K.Kelviz has the ability to designate plots that use lines and line data from other plots. This allows for multiple presentations of the same dataset in your figure.
To do this, one must first create a new, empty plot in the figure (this can be done via the Configure Figure Layout dialog - see Plot Location and Layout In The Figure, above), and then go to that plot's tab in the Configure Linesets dialog.
Check the Use lines from another plot checkbox to turn on the option to show another plot's data within this plot as well. You will also need to select the plot whose data you want to share with this plot - all plots that currently have data imported into them will be listed.
Plots that use lines and line data from other plots have their own view limits (see Zooms and Views, below), annotations (see Annotations, immediately below), tick mark options (see Tick Marks, immediately above), and horizontal lines (see Horizontal Lines, above). They do not have a Legend. Any data lines and/or marker maps (see Marker Map Overlays, below) are shared with the original "parent" plot, and their appearance must be configured within that plot - you cannot have a line appear to look one way in one plot and look differently in another.
Annotations are text labels used to highlight and label data points of interest. Kelviz has several different options for creating and manipulating annotations, and can create them either one at a time or several at a time.
By default, annotation text consists of:
These can be modified; see Modifying Annotation Defaults, below.
New annotations can be quickly created by going into Annotate Point Mode. This is done by clicking the toolbar button illustrated to the right.
In Annotate Point Mode, you can click on or near data points in a plot to create annotations for them. To leave Annotate Point Mode, click this button again.
Alternatively, you can easily select a peak point or a valley point using one of the Annotate Peak or Annotate Valley modes. These are accessed respectively by clicking one of the toolbar buttons shown to the right.
When one of these modes is turned on, you can click and drag to select a region on a plot containing a peak (or valley) that you want annotated. The data point(s) with the highest (or lowest) PPL value within that region will be annotated.
NOTE: If you have two peaks with the exact same PPL value within the same selected region, Kelviz has no way of figuring out which of the two peaks you actually want, and so they will both be annotated. The same goes for any valleys. Keep this in mind when making your selection!
To leave Annotate Peak or Annotate Valley mode, click the respective button again.
Annotations can also be created en masse using the Annotate Threshold function. Access it by clicking the button illustrated to the right, or by going to the Edit menu and selecting Annotate Threshold. You will get a dialog box as follows:
You will need to provide a threshold value and a threshold mode. The value is the Y-axis position (PPL value) that will serve as the threshold above or below which annotations will be created. The mode designates whether or not we're creating annotations above or below the threshold, and whether or not we just want peaks (or valleys), the boundaries of a peak, or all data points.
Annotations labels can be moved or edited to include other text.
To move an annotation label, you must go into Annotation Movement Mode. This can be done by clicking on the toolbar button illustrated to the right.
Once this mode is turned on, you can click on the text of any annotation and drag it to wherever you would like it to be positioned in the plot. When done moving annotations, click on the toolbar button again to turn this mode off.
Alternatively, you can opt to use Kelviz's automatic annotation layout functionality. Do this by clicking on the Automatically Layout Annotations toolbar button (illustrated to the right) or by going to the Edit menu and selecting Automatically Layout Annotations. You will get a dialog box as follows:
For other annotation editing functions, you can right-click on the annotation to get an editing menu, as illustrated below:
The Remove Annotation menu option deletes the annotation.
Edit Annotation brings up a dialog as illustrated below:
All annotations can be deleted at once with one command. Go to the Edit menu and select Remove All Annotations. You will be prompted to confirm this action, as it cannot be undone.
Default options for annotations are managed via the Configure Annotations dialog. To reach it, go to the Options menu and select Configure Annotations.
Annotation display is also subject to some performance-related defaults. To manage these, go to the Options menu and select Performance to reach the Performance dialog.
NOTE: These options are saved in GRX files and are specific to those; they are restored to defaults with each new GRX file you create in Kelviz.
Kelviz allows you to change whatever portion of a plot is displayed by way of panning around and zooming in and out; this can be done via manually entering values, or even interactively. Each "step" along the way - a pause while panning around, each point where one is zoomed in, et cetera - is called a view, and the history of such views is saved so that you can navigate back and forth between them. There is also a home view - a special "zoom out" in which all data points plotted are visible.
Viewing options are normally handled through the toolbar, as follows:
Home View
Previous View
Next View
Pan Modex key on the keyboard while dragging with the left mouse button, the plot will only drag horizontally (along the X axis). The y key can be similarly used to only drag vertically (along the Y axis).
Zoom To Region Mode
Zoom To X-Axis Limits Mode
Zoom To Y-Axis Limits Mode
Zoom To ChromosomeA precise view can also be set using the View Limits dialog. Access this by going to the Options menu and selecting Set x-axis, y-axis limits.
Marker Map overlays are an additional means by which marker maps can be displayed in your plots and marker names can be added to your annotations. They show up as symbols overlaid on the lines plotted in your plot.
You will likely have the necessary data file as part of your Kelvin analysis - it's the required "map file".
Adding a new marker map overlay is done by going to the Insert menu and selecting Overlay Marker Map. You will be prompted for the filename for your marker map, and then presented with the Marker Map File Format dialog to tell Kelviz a little about your marker map.
NOTE: Marker map overlays are only added to lines that are currently in the plot at the time they're imported. If you add new data lines after the marker map overlay has been added, they will NOT be overlaid. You will have to delete and readd the marker map if you want them overlaid.
Marker map appearance (the size, color, and symbol shape) can be changed after importing by accessing the Configure Marker Map dialog. This is reached by going to the Options menu and selecting Configure Marker Map.
Tabs are presented for each plot in your figure, and each such tab presents a row of controls for each marker map present in that plot. The functions of each control are identical to their counterparts in the Marker Map File Format dialog, above.
Images of Kelviz figures can be created at any time using the Export Image function. This can be done by clicking on the Export Figure To Image toolbar button (illustrated to the right), or by going to the File menu and selecting Export Figure To Color Image. You will be prompted for a filename.
Images can also be exported as grayscale images; do this by going to the File menu and selecting Export Figure To Grayscale Image.
Kelviz has the ability to create image collages consisting of tables of subplots, for when you want one plot per lineset (genome) or one per chromosome from a single given plot in the figure. This table layout can also be applied to existing plots in the figure. Collages can be saved as images, or saved as Kelviz GRX files for further tweaking after generation. To create such a collage, go to the File menu and select Create Collage Table From Figure.
For each (sub)plot, the following additional options are provided:
Any text that shows up in the figure - the figure title, axis titles, annotation labels, et cetera - can use TeX markup to display limited font formatting and mathematical symbols and expressions.
Specify this by starting and ending your test with dollar signs. For example, alpha > beta will produce plain text, while $\alpha > \beta$ will produce the greek letters, as shown:
becomes 
You can use several other TeX symbols, such as \infty, \leftarrow, and \sum:
becomes 
Other TeX symbols that can be used are listed on the matplotlib website.
To make subscripts and superscripts, use the _ and ^ symbols, respectively:
becomes 
For some symbols, using a subscript means the text is placed underneath the symbol, and the superscript is placed above the symbol. This applies to symbols for which that behavior makes sense. Note how braces are used for subscripts or superscripts that are longer than one character:
becomes 
The default font is italics. To use a different font, enclose the text you want in a different font in a font command, which essentially means type the font symbol, then the text you want in that font in braces. For example, to write the word 'sin' in a roman font:
becomes 
Other fonts include roman \rm, italics \it, calligraphy \cal, and typewriter \tt:
becomes 
There are command line options available to perform most actions in Kelviz. The syntax is as follows:
./kelviz.py <command1> <args1> <command2> <args2> ...python kelviz.py <command1> <args1> <command2> <args2> ...Kelviz.app/Contents/MacOS/kelviz <command1> <args1> <command2> <args2> ...%programfiles%\kelviz.exe <command1> <args1> <command2> <args2> ...If a command appears multiple times, generally the last occurrence will
override any subsequent commands, with the notable exception of commands that
work with files (-open, -save, -export, -import_data, and so forth).
Commands are performed in the order that they are specified, except in some special cases:
-open is always performed first.-save and -export are always performed last.-min_gridsize is always performed near-last - only -save and -export
are performed after it.Starting with version 3.0.0, Kelviz allows you to have multiple plots within a
single figure. Consequently, many command arguments now have a [plot=<name>]
argument as their first possible argument. This indicates that that command
expects to be given a reference to a plot that it's supposed to configure. This
can be done either by providing the argument plot=<name> as the first
argument to that command, or preceding that command with the -plot <name>
command (which will also affect all following commands).
For both of the above, <name> must be a valid plot name. Valid plot
names are the lowercase letters "a" through "z", in order.
If a plot is not specified, plot "a" is assumed.
Some commands that require that a plot be specified can take the argument
plot=ALL, indicating that the command in question should be applied to every
plot in the figure. Each command's documentation will indicate if this is
possible.
Command arguments that ask for a lineset_id expect the internal ID of a
lineset, but can also (sometimes) work with the name of a lineset. A lineset
ID is specified when the data creating that lineset is initially imported and
cannot be changed afterward.
Command arguments that ask for a line_id expect a special ID type, but can
also (sometimes and unreliably) work with the name of a line. Line IDs consist
of the name of the lineset the line is part of followed by __LINE_ followed
by the chromosome number of that line.
Example 1: the line for chromosome 13 of lineset Example has the ID
Example__LINE_13
Example 2: the line for chromosome X of lineset OtherExample has the ID
OtherExample__LINE_23
Command arguments that are column indices start at 1, not 0.
Some command line arguments ask to specify a color. There are three options available to specify color:
-version-help-open <filename><filename> -- Path to GRX file.<filename>-open above.<filename> -- Path to GRX file.-save <filename><filename> -- Path to a file. If the .grx extension is not present in
at the end of the filename, it is added on automatically.-noshow-plot <name>plot=<name>
as their first argument) are intended to configure the named plot. See
"Special Arguments", above.<name> - A plot name. Valid plot names are lowercase letters "a"
through "z", in order.-no_warningsStarting with version 2.2.0, Kelviz has a "command files" capability - you can give it text files that consist of one command per line and it will execute them.
Lines in a command file starting with # are ignored.
There are two ways you can take advantage of command files:
.kelvizcmd in the directory you're executing
Kelviz in and putting your commands there,-command_file option (see below)Both can be used simultaneously, and concurrently with other command line options, and you can add multiple command files. The order of precedence is as follows:
.kelvizcmd commands are added first-command_file commandfiles (in the order that they're specified
on the command line)Then each command is performed in the order it's specified, subject to the
special cases listed above in re: -open, -save, and -export.
-command_file <filename><filename> -- The name of the text file containing the command line
arguments.These add new lines and linesets to a plot.
All options that start with -data_ are dependent on a corresponding
-import_data command, which they must follow. If you're importing multiple
data files (or multiple sets of data from the same file), make sure that each
set of -data_ commands only follows its respective -import_data and no
other.
-import_plot <filename> <sourceplotname><filename> -- Path to the GRX file from which we are importing our plot.<sourceplotname> -- The name of the plot we'll be loading from the GRX
file.-import_data [plot=<name>] <filename>[plot=<name>] -- Optional; specifies which plot we're importing data into.
(See Special Arguments, above.)<filename> -- Path to the datafile we're importing.-data_pos_col <column>position, pos, cm, kosambi, haldane, position1, position2.-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<column> -- Column with chromosome position values (x-axis). Specified by
name of column in file (if there's a header line) OR column index number.-data_ppl_col <column>ppl, ppl(ld), ppld|l, ppld-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<column> -- Column with PPL values (x-axis). Specified by name of column
in file (if there's a header line) OR column index number.-data_chr_col <column>chromosome or chr and use it.
If we can't find one of those, we check -data_chr_num (see below). If
that's left out, we assume that each blank newline-separated "section"
constitutes a new chromosome.-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<column> -- Column with chromosome numbers. Specified by name of column
in file (if there's a header line) OR column index number.-data_lineset <lineset_id>-data_lineset_replace below.-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<lineset_id> -- Text ID for the lineset we're adding data to. (See
Special Arguments, above.) If the lineset doesn't exist, it will be
created. No spaces or special punctuation characters are permitted in this
ID!-data_overlap <on/off>-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<on/off> -- Turn this option ON or OFF. Defaults to ON if we're creating
a new lineset for an existing plot, and OFF otherwise.-data_lineset_replace <on/off>-data_lineset above).-data_lineset, -data_overlap, -data_chr_prefix, -data_chr_postfix,
-data_line_color, -data_color_per_line-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<on/off> -- Turn this option ON or OFF. Defaults to ON if this data's
lineset ID (see -data_lineset above) already exists, and OFF otherwise.-data_use_header_line <on/off>-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<on/off> -- Turn this option ON or OFF. Defaults to ON.-data_chr_num <chr_num>-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<chr_num> -- Chromosome number this text file has data for.
Integer value (1-24) only.-data_chr_select <chr1> <chr2> ...-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<chrX> -- Series of chromosome numbers to load.-data_chr_prefix <prefix>-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<prefix> -- Prefix for each chromosome number.-data_chr_postfix <postfix>-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<postfix> -- Postfix for each chromosome number.-data_metadata_cols <column1> <column2> ...-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<columnX> -- Series of columns that contain metadata we want to include.
Specified by name of column in file (if there's a header line) OR column
index number.-data_line_color <color>-lineset_color and -line_color
options if they appear!-data_cycle_color_by_lines below.-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<color> -- The color desired for the line(s).-data_color_per_line <on/off>-data_line_color, -lineset_color, and -line_color
options if they appear!-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<on/off> -- Turn this option ON or OFF. Defaults to OFF.-data_missing_value_tokens <token1> <token2> ...-import_data and otherwise ignored. Must come after the
-import_data it is intended to configure and no other.<tokenX> -- Series of numbers or strings of any kind indicating what
data values indicate lines to be skipped.These change lines and linesets that already exist in a plot.
All of these commands require that a plot be specified and/or a lineset_id or line_id be specified; see Special Arguments (above) for information on these arguments.
-use_other_plot_lines [plot=<name>] <plot>[plot=<name>] -- Optional; specifies the plot that will be displaying data
lines from another plot. (See Special Arguments, above.)<plot> -- The name of the plot whose lines will be reused in another
plot. Valid plot names are the lowercase letters "a" through "z", in order.-lineset_name [plot=<name>] <lineset_id> <name>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<name> -- The name. (Be sure to put quotes around it!)-lineset_color [plot=<name>] <lineset_id> <color>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<color> -- The color desired for the lines.-lineset_linestyle [plot=<name>] <lineset_id> <style>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<style> -- The style desired for the lines.solid, dashed, dotted, dash-dot, steps, no line.solid.-lineset_thickness [plot=<name>] <lineset_id> <thickness>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<thickness> -- How thick the chromosome lines should be. Integer values
only. Default is 2.-lineset_symbol [plot=<name>] <lineset_id> <symbol>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<symbol> -- Name of the symbol type. (Be sure to put quotes around the
name!)no symbol, caret down, caret left, caret right,
caret up, circle, diamond, hexagon 1, hexagon 2,
horizontal line, octagon, pentagon, pixel, plus, point,
square, star, thin diamond, tick down, tick left, tick right,
tick up, tripod down, tripod left, tripod right, tripod up,
triangle down, triangle left, triangle right, triangle up,
vertical line, xno symbol.-lineset_symbol_size [plot=<name>] <lineset_id> <size>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<size> -- Size of the symbol (approximately the radius in pixels).
Integer values only. Default is 6.-lineset_zorder [plot=<name>] <lineset_id> <order>[plot=<name>] -- Optional; specifies which plot the lineset is in. (See
Special Arguments, above.)<lineset_id> -- Text ID for the lineset we're configuring. (See Special
Arguments, above.)<order> -- Order in which to draw this line. Integer values only.
Default is in sequence from first lineset imported to last.-line_name [plot=<name>] <line_id> <name>-show_line_names, below), and (with the
-legend_show_linesets option) optionally in the Legend.[plot=<name>] -- Optional; specifies which plot the line is in. (See
Special Arguments, above.)<line_id> -- Text ID of the line we're configuring. (See Special
Arguments, above.)<name> -- The name. (Be sure to put quotes around it!)-line_color [plot=<name>] <line_id> <color>-lineset_color if
it's specified![plot=<name>] -- Optional; specifies which plot the line is in. (See
Special Arguments, above.)<line_id> -- Text ID of the line we're configuring. (See Special
Arguments, above.)<color> -- The color desired for the line.-line_linestyle [plot=<name>] <line_id> <style>-lineset_linestyle if it's specified![plot=<name>] -- Optional; specifies which plot the line is in. (See
Special Arguments, above.)<line_id> -- Text ID of the line we're configuring.<style> -- The style of the line.solid, dashed, dotted, dash-dot, steps, no line.solid if the lineset the line is part of hasn't been changed
and is equal to that lineset's style otherwise.-line_thickness [plot=<name>] <line_id> <thickness>-lineset_thickness if it's specified![plot=<name>] -- Optional; specifies which plot the line is in. (See
Special Arguments, above.)<line_id> -- Text ID of the line we're configuring. (See Special
Arguments, above.)<thickness> -- How thick the line should be. Integer values only.
Default is 2.-line_symbol [plot=<name>] <line_id> <symbol>-lineset_symbol if it's specified![plot=<name>] -- Optional; specifies which plot the line is in. (See
Special Arguments, above.)<line_id> -- Text ID of the line we're configuring. (See Special
Arguments, above.)<symbol> -- Name of the symbol type. (Be sure to put quotes around the
name!)no symbol, caret down, caret left, caret right,
caret up, circle, diamond, hexagon 1, hexagon 2,
horizontal line, octagon, pentagon, pixel, plus, point,
square, star, thin diamond, tick down, tick left, tick right,
tick up, tripod down, tripod left, tripod right, tripod up,
triangle down, triangle left, triangle right, triangle up,
vertical line, xno symbol if the lineset the line is part of hasn't been
changed and is equal to that lineset's symbol otherwise.-line_symbol_size [plot=<name>] <line_id> <size>-lineset_symbol_size if it's specified![plot=<name>] -- Optional; specifies which plot the line is in. (See
Special Arguments, above.)<line_id> -- Text ID of the line we're configuring. (See Special
Arguments, above.)<size> -- Size of the symbol (approximately the radius in pixels).
Integer values only. Default is 6 if the lineset the line is part of
hasn't been changed and is equal to that lineset's symbol size otherwise.-hline [plot=<name>] <num1> <num2> ...[plot=<name>] -- Optional; specifies which plot we're creating a
horizontal line in. (See Special Arguments, above.)<numX> -- Series of y-values (PPL values) of the line(s) to be added.These change options that affect the entire figure.
-comment <comment><comment> -- The comments. (Be sure to put quotes around them!)-figure_title <title><title> -- Figure title. (Be sure to put quotes around it!)-figure_title_text_size <size><size> -- Font size, in points. Integer values only. Default is 14.-plot_autotitles <on/off><on/off> -- Turn this option ON or OFF. Defaults to ON.-serif_fonts <on/off><on/off> -- Turn this option ON or OFF. Defaults to OFF.-show_figure_legend <on/off>-show_legend by automatically disabling all plot-
specific legends!<on/off> -- Turn this option ON or OFF. Defaults to OFF.-figure_legend_location <loc><loc> -- The desired legend location. (Be sure to put quotes around it!)center left, center right, in grid.center right.-figure_legend_text_size <size><size> -- Font size, in points. Integer values only. Default is 14.-figure_legend_gridloc <rowstart> <rowend> <colstart> <colend>-figure_legend_location is set to in grid!<rowstart> -- Row that the legend should start in in the layout grid.
Integer values only.<rowend> -- Row that the legend should end in in the layout grid. Integer
values only.<colstart> -- Column that the legend should start in in the layout grid.
Integer values only.<colend> -- Column that the legend should end in in the layout grid.
Integer values only.-ann_ppl_precision <precision><precision> -- The precision level to use. The keyword default can be
used to set default precision mode as described above; otherwise, integer
values only.-ann_pos_precision <num><num> -- Number of decimal places to show. Default is 0.-ann_show_percent <on/off><on/off> -- Turn this option ON or OFF. Defaults to ON.-ann_same_color <on/off>-ann_default_color, below).<on/off> -- Turn this option ON or OFF. Defaults to OFF.-ann_default_color <color>-ann_color, below)<color> -- The desired default annotation color. Default is "black".-ann_default_fontsize <size>-ann_fontsize,
below)<size> -- Font size, in points. Integer values only. Default is 12.-ann_use_metadata <on/off>-data_metadata_cols above or
-markermap_metadata_cols below), this toggles whether or not to use that
metadata in place of the position in annotation text.<on/off> -- Turn this option ON or OFF. Defaults to ON.-figure_size <width> <height><width> -- Width of the figure, in inches. Defaults to 10.<height> -- Height of the figure, in inches. Defaults to 8.-figure_padding <padding><padding> -- The desired amount of padding. Defaults to 1.-min_gridsize <rows> <cols><rows> -- Number of rows. Integer values only. Default is 1.<cols> -- Number of columns. Integer values only. Default is 1.-export_dpi <dpi><dpi> -- DPI (dots per inch) value for exported images. Integer values
only. Defaults to 300.These change options that affect a single plot or multiple plots.
-plot_title [plot=<name>] <title>[plot=<name>] -- Optional; specifies which plot we're changing the title
for. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<title> -- Plot title. (Be sure to put quotes around it!)-plot_title_text_size [plot=<name>] <size>[plot=<name>] -- Optional; specifies which plot we're changing the title
font size for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<size> -- Font size, in points. Integer values only. Default is 12.-xlabel [plot=<name>] <label>[plot=<name>] -- Optional; specifies which plot we're changing the x-axis
label for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<label> -- x-axis label. (Be sure to put quotes around it!)-ylabel [plot=<name>] <label>[plot=<name>] -- Optional; specifies which plot we're changing the y-axis
label for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<label> -- y-axis label. (Be sure to put quotes around it!)-axis_text_size [plot=<name>] <size>[plot=<name>] -- Optional; specifies which plot we're changing the axis
label font size for. Can change all plots simultaneously with plot=ALL.
(See Special Arguments, above.)<size> -- Font size, in points. Integer values only. Default is 12.-xlabel_padding [plot=<name>] <padding>[plot=<name>] -- Optional; specifies which plot we're adding xlabel
padding to. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<padding> -- Padding amount, in points. Integer values only. Default is 0.-bgcolor [plot=<name>] <color>[plot=<name>] -- Optional; specifies which plot we're changing the
background color for. Can change all plots simultaneously with plot=ALL.
(See Special Arguments, above.)<color> -- Background color. Default is "white" (#FFFFFF)-show_legend [plot=<name>] <on/off>-show_figure_legend, above![plot=<name>] -- Optional; specifies which plot we're turning the legend
on or off for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to OFF if there's only
one lineset and ON if we have more than one lineset.-show_legend_frame [plot=<name>] <on/off>[plot=<name>] -- Optional; specifies which plot we're toggling the legend
frame for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to ON.-legend_show_linesets [plot=<name>] <on/off>[plot=<name>] -- Optional; specifies which plot we're changing the legend
listing for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to ON.-legend_location [plot=<name>] <loc>[plot=<name>] -- Optional; specifies which plot we're changing the legend
location for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<loc> -- The desired legend location. (Be sure to put quotes around the
name!)upper right, upper left, upper center,
lower right, lower left, lower center, center left,
center right, center.upper right.-legend_text_size [plot=<name>] <size>[plot=<name>] -- Optional; specifies which plot we're changing the legend
font size for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<size> -- Font size, in points. Integer values only. Default is 14.-show_line_names [plot=<name>] <on/off>[plot=<name>] -- Optional; specifies which plot we're toggling the
chromosome number labels for. Can change all plots simultaneously with
plot=ALL. (See Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to ON.-label_text_size [plot=<name>] <size>[plot=<name>] -- Optional; specifies which plot we're changing the label
font size for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<size> -- Font size, in points. Integer values only. Default is 12.-use_condensed_line_name_font [plot=<name>] <on/off>[plot=<name>] -- Optional; specifies which plot we're toggling the
condensed font option for. Can change all plots simultaneously with
plot=ALL. (See Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to OFF.-chr23_rename_X [plot=<name>] <on/off>[plot=<name>] -- Optional; specifies which plot we're toggling the rename
option for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to ON.-chr24_rename_Y [plot=<name>] <on/off>[plot=<name>] -- Optional; specifies which plot we're toggling the rename
option for. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)<on/off> -- Turn this option ON or OFF. Defaults to ON.-plot_gridloc [plot=<name>] <rowstart> <rowend> <colstart> <colend>[plot=<name>] -- Optional; specifies which plot we're changing the
location of. (See Special Arguments, above.)<rowstart> -- Row that the plot should start in in the layout grid.
Integer values only.<rowend> -- Row that the plot should end in in the layout grid. Integer
values only.<colstart> -- Column that the plot should start in in the layout grid.
Integer values only.<colend> -- Column that the plot should end in in the layout grid.
Integer values only.-xlimits [plot=<name>] <xmin_chr> <xmin_pos> <xmax_chr> <xmax_pos>[plot=<name>] -- Optional; specifies which plot we're changing view limits
for. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<xmin_chr> -- Name of the chromosome that the minimum X position should
appear along.<xmin_pos> -- The minimum X value, specified as a position along
<xmin_chr>.<xmax_chr> -- Name of the chromosome that the maximum X position should
appear along.<xmax_pos> -- The maximum X value, specified as a position along
<xmax_chr>.-ylimits [plot=<name>] <ymin> <ymax>[plot=<name>] -- Optional; specifies which plot we're changing view limits
for. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<ymin> -- The minimum Y value. Real number values only.<ymax> -- The maximum Y value. Real number values only.-view_limits [plot=<name>] <xmin_chr> <xmin_pos> <xmax_chr> <xmax_pos> <ymin> <ymax>-xlimits and -ylimits commands
listed above. See those commands for descriptions of this command's
parameters.-zoom_chr [plot=<name>] <chr_num>[plot=<name>] -- Optional; specifies which plot we're changing view limits
for. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<chr_num> -- The number of the chromosome to zoom in to. Integer values
only.-tick_text_size [plot=<name>] <size>[plot=<name>] -- Optional; specifies which plot we're changing the tick
mark font size for. Can change all plots simultaneously with plot=ALL.
(See Special Arguments, above.)<size> -- Font size, in points. Integer values only. Default is 11.-tick_mode [plot=<name>] <mode>default) is designed to be used for genome-wide
chromosome plots.base-pairs). The tick interval is 500,000, and tick marks are
always shown at even multiples of the interval.[plot=<name>] -- Optional; specifies which plot we're changing tickmark
parameters for. (See Special Arguments, above.)<mode> -- The tick mode desired.default, base-pairs, custom.default.-tick_interval <size>-tick_mode custom above and otherwise ignored.<size> -- Interval size. Real number values only.-tick_placement <placement>-tick_mode custom above and otherwise ignored.<placement> -- The desired placement option.even_multiples, first_position.even_multiples.-tick_scientific_notation <on/off>-tick_mode custom above and otherwise ignored.<on/off> -- Turn this option ON or OFF. Defaults to OFF.-tick_precision <num>-tick_mode custom above and otherwise ignored.<num> -- Number of decimal places to show. Integer values only.-tick_include_first_position <on/off>-tick_mode custom above and otherwise ignored.<on/off> -- Turn this option ON or OFF. Defaults to OFF.-tick_include_last_position <on/off>-tick_mode custom above and otherwise ignored.<on/off> -- Turn this option ON or OFF. Defaults to OFF.These add marker map overlays to a plot.
All options that start with -markerdata_ are dependent on a corresponding
-import_markermap_data command, which they must follow. If you're adding
multiple marker maps to your plot, make sure that each set of -markerdata_
commands only follows its respective -import_markermap_data and no other.
-import_markermap_data [plot=<name>] <filename>[plot=<name>] -- Optional; specifies which plot we're adding the marker
map to. (See Special Arguments, above.)<filename> -- Path to the marker map datafile we're importing. The
filename (with the path and extension stripped) also serves as the default
name of the marker map.-markerdata_chr_col <column>chromosome or chr and use it.
If that's left out, we assume that each blank newline-separated "section"
constitutes a new chromosome.-import_markermap_data and otherwise ignored. Must come
after the -import_markermap_data it is intended to configure and no other.<column> -- Column with chromosome numbers. Specified by name of column
in file (if there's a header line) OR column index number.-markerdata_pos_col <column>position, pos, cm, kosambi, haldane, position1, position2.-import_markermap_data and otherwise ignored. Must come
after the -import_markermap_data it is intended to configure and no other.<column> -- Column with chromosome position values. Specified by name of
column in file (if there's a header line) OR column index number.-markerdata_use_header_line <on/off>-import_markermap_data and otherwise ignored. Must come
after the -import_markermap_data it is intended to configure and no other.<on/off> -- Turn this option ON or OFF. Defaults to ON.-markerdata_metadata_cols <column1> <column2>-data_metadata_cols command,
above).-import_markermap_data and otherwise ignored. Must come
after the -import_markermap_data it is intended to configure and no other.<columnX> -- Series of columns that contain metadata we want to include.
Specified by name of column in file (if there's a header line) OR column
index number.-marker_map_name [plot=<name>] <oldname> <newname>-marker_map_ commands.[plot=<name>] -- Optional; specifies which plot contains the marker map
we're renaming. (See Special Arguments, above.)<oldname> - The existing marker map name. By default, this is the name of
the datafile used to create the marker map (example: a marker map datafile
named "markers2.txt" would, on import, be given the name "markers2").<newname> - The name you want to give to this marker map. No spaces or
special punctuation characters are permitted in this name!-marker_map_size [plot=<name>] <name> <size>[plot=<name>] -- Optional; specifies which plot contains the marker map
we're changing the symbol size for. (See Special Arguments, above.)<name> -- The name of the set of markers you want to change.<size> -- The desired marker symbol size.-marker_map_color [plot=<name>] <name> <color>[plot=<name>] -- Optional; specifies which plot contains the marker map
we're changing the color for. (See Special Arguments, above.)<name> -- The name of the set of markers you want to change.<color> -- The desired marker symbol color.-marker_map_symbol [plot=<name>] <name> <symbol>[plot=<name>] -- Optional; specifies which plot contains the marker map
we're changing the symbol for. (See Special Arguments, above.)<name> -- The name of the set of markers you want to change.<symbol> -- Name of the symbol type. (Be sure to put quotes around the
name!)<symbol> -- Name of the symbol type. (Be sure to put quotes around the
name!)no symbol, caret down, caret left, caret right,
caret up, circle, diamond, hexagon 1, hexagon 2,
horizontal line, octagon, pentagon, pixel, plus, point,
square, star, thin diamond, tick down, tick left, tick right,
tick up, tripod down, tripod left, tripod right, tripod up,
triangle down, triangle left, triangle right, triangle up,
vertical line, xo.These allow us to create annotations in a plot, with optional different styles.
Annotation styling commands (-ann_color, -ann_fontsize, -ann_metadata, and
-ann_always_visible) are dependent on one of the corresponding annotation
creation commands (-ann_threshold, -ann_peak, and -ann_valley), which
they must follow. If you're creating multiple annotations, make sure that each
styling command only follows its respective creation command and no other.
-ann_autolayout [plot=<name>][plot=<name>] -- Optional; specifies which plot we're having lay out
annotations. Can change all plots simultaneously with plot=ALL. (See
Special Arguments, above.)-ann_threshold [plot=<name>] <type> <threshold>[plot=<name>] -- Optional; specifies which plot we're adding annotations
to. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<type> -- One of peak, valley, all_above, all_below, or
peak_boundary.peak annotates all peaks above the threshold.valley annotates all valleys below the threshold.all_above annotates all data points above the threshold.all_below annotates all data points below the threshold.peak_boundary annotates the boundaries of any peaks crossing the
threshold.<threshold> -- The threshold value. Real number values only.-ann_threshold_lineset <lineset_id>-ann_threshold
above) should be added only to the specified lineset ID.-ann_threshold and otherwise ignored. Must come after the
-ann_threshold it is intended to configure and no other.<lineset_id> -- Text ID for the lineset we're restricting annotation
creation to. (See Special Arguments, above.)-ann_peak [plot=<name>] <xstart_chr> <xstart_pos> <xend_chr> <xend_pos>[plot=<name>] -- Optional; specifies which plot we're adding annotations
to. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<xstart_chr> -- Name of the chromosome that the starting X position
should appear along.<xstart_pos> -- The starting X value, specified as a position along
<xstart_chr>.<xend_chr> -- Name of the chromosome that the ending X position should
appear along.<xend_pos> -- The ending X value, specified as a position along
<xend_chr>.-ann_valley [plot=<name>] <xstart_chr> <xstart_pos> <xend_chr> <xend_pos>[plot=<name>] -- Optional; specifies which plot we're adding annotations
to. Can change all plots simultaneously with plot=ALL. (See Special
Arguments, above.)<xstart_chr> -- Name of the chromosome that the starting X position
should appear along.<xstart_pos> -- The starting X value, specified as a position along
<xstart_chr>.<xend_chr> -- Name of the chromosome that the ending X position should
appear along.<xend_pos> -- The ending X value, specified as a position along
<xend_chr>.-ann_color <color><color> -- The desired color of the annotation or annotations.-ann_fontsize <size><size> -- Font size, in points. Integer values only. Default is 12.-ann_metadata <on/off><on/off> -- Turn this option ON or OFF. Defaults to ON.-ann_always_visible <on/off>chr collage, or having used -zoom_chr), or if they
should remain always visible.<on/off> -- Turn this option ON or OFF. Defaults to ON.These create rendered images of our plots.
All options that start with -collage_ are dependent on a corresponding
-export_collage command, which they must follow. If you're creating multiple
subplot collages, make sure that each set of -collage_ commands only follows
its respective -export_collage and no other.
-export <filename>.png, .tif, .eps, .svg, and .pdf. If no
extension is provided, .png is assumed by default.<filename> -- Desired filename for the image.-export_collage [plot=<name>] <type> <filename>chr type - or by lineset -
lineset type), or by selecting existing plots within the figure. The
resulting selection of plots is then rearranged into a tabular form and
given an in-grid figure-wide legend.[plot=<name>] -- Optional; specifies which plot we're creating a collage
from. Needed for chr and lineset type collages. (See Special Arguments,
above.)<type> -- The type of subplots desired.chr (individual chromosomes), lineset (individual
linesets), and plot (existing plots in the figure).<filename> -- Desired filename for the collage. Can be an image file or a
Kelviz GRX file; the format will be determined by the filename extension.-collage_figure_size <width> <height>-collage_columns, below) and as many rows as needed to fit all the
subplots.-collage_plot_size, below. (Note also that this command overrides
-collage_plot_size!)<width> -- Width of the collage, in inches.<height> -- Height of the collage, in inches.-collage_plot_size <width> <height>chr and lineset collages, by default, will attempt to calculate a plot
size based on the amount of space the original source plot being split up
into subplots took up. plot collages will calculate a plot size based on
the original figure size.-collage_figure_size; see above!<width> -- Width of each plot, in inches.<height> -- Height of each plot, in inches.-collage_columns <columns><columns> -- The number of columns desired. Default is 2.-collage_include <id1> <id2> ...<idX> -- Series of IDs to include in the collage.chr-type collages, this is specified by chromosome numbers ("1 2 3 5
8 13"). Ranges are also possible ("1-5 6 9-12").lineset-type collages, this is specified by lineset ID (see
information on lineset IDs, above.)plot-type collages, this is specified by plot name ("a b d f").-collage_legend_location <id> <loc>chr and lineset type collages, this indicates that we want a
particular subplot (identified by ID) to have a non-default legend
location. By default, every subplot uses the parent plot's legend location
(specified by -legend_location, above).plot-type collage.<id> -- The ID of the subplot for which we are specifying a legend
location.chr-type collages, this is specified by chromosome numbers ("1 2 3 5
8 13").lineset-type collages, this is specified by lineset ID (see
information on lineset IDs, above.)<loc> -- The desired legend location. (Be sure to put quotes around the
name!)upper right, upper left, upper center,
lower right, lower left, lower center, center left,
center right, center.-legend_location; if that option has not
been specified, the default is upper right.<on/off> -- Turn this option ON or OFF. Defaults to ON.-collage_autotitles <on/off>chr and lineset type collages, this toggles whether or not we want
each plot to have automatic titles ("(a)", "(b)", "(c)", etc. - the
default) or if they should have no titles at all.<on/off> -- Turn this option ON or OFF. Defaults to ON.-collage_title <id> <title>chr and lineset type collages, this indicates that we want a
particular subplot (identified by ID) to have its own particular title. By
default, subplots are given automatic titles; those have to be turned off
for this option to be effective (see -collage_autotitles, immediately
above).<id> -- The ID of the subplot for which we are specifying a title.chr-type collages, this is specified by chromosome numbers ("1 2 3 5
8 13").lineset-type collages, this is specified by lineset ID (see
information on lineset IDs, above.)<title> -- Plot title. (Be sure to put quotes around it!)-collage_ylimits <method>chr and lineset type collages, this specifies how the Y-axis limits
should be determined for each subplot.<method> -- One of home or current.home means that default Y-axis limits will be used (as if the Home button
had been pressed on the toolbar).current uses the parent plot's current Y-axis limits.-collage_custom_ylimits <id> <ymin> <ymax>chr and linesert type collages, this specifies custom Y-axis view
limits for a specific subplot (identified by ID).<id> -- The ID of the subplot for which we are specifying Y-axis view
limits.chr-type collages, this is specified by chromosome numbers ("1 2 3 5
8 13").lineset-type collages, this is specified by lineset ID (see
information on lineset IDs, above.)<ymin> -- The minimum Y value. Real number values only.<ymax> -- The maximum Y value. Real number values only.-collage_separate_legend <on/off>in grid position option. Turn this option off to let each plot have
its own legend.<on/off> -- Turn this option ON or OFF. Defaults to ON.Some commands or command formats continue to function for backwards
compatibility. They have since been replaced, and may go away in future
versions of Kelviz. They can be found in deprecated.md in the Kelviz
documentation directory.
Alternatively, click here for a listing.
Open GRX File
Import Data From Text File
Save GRX File
Export Figure To Image
Add or Remove Horizontal Lines Zoom To Chromosome Home View Previous View Next View Pan Mode Zoom To Region Mode Zoom To X-Axis Limits Mode Zoom To Y-Axis Limits Mode
Annotate Point Mode
Annotate Peak Mode
Annotate Valley Mode
Annotate Threshold
Annotation Movement Mode
Automatically Layout Annotations