Deprecated Commands (Avoid Use)

These commands or command formats still presently function for backwards compatibility. They have since been replaced, and may go away in future versions of Kelviz.

-open <type> <filename> 
    * DEPRECATED; see -import_data
    <type> -- text, grx, what type of file to open
    <filename> -- path to file

    * all these commands are used when <type> is text
    * command are optional unless otherwise specified

    -pos_col <num>
        * DEPRECATED; see -import_data
        * column index of column with position values
        <num> -- integer, the column index
        * required

    -ppl_col <num>
        * DEPRECATED; see -import_data
        * column index of column with ppl values
        <num> -- integer, the column index
        * required

    -header_lines <num>
        * DEPRECATED; see -data_use_header_line
        * the number of lines at the top of the file that constitute the 
          header.
        * the header will be ignored when processing the file.
        <num> -- integer, the number of lines

    -chr_num <num>
        * DEPRECATED; see -data_chr_num
        * if text file has info about only one chr, tells program what the 
          chr number of that chr is
        <num> -- integer, the number of the chr in the file

    -chr_col <num>
        * DEPRECATED; see -data_chr_col
        * column index of column with chr number
        <num> -- integer, the column index
        * optional, if left out, will assume first set of values is chr1, 
          then second set of values is chr2, etc.

    -chr_select <num1> <num2> etc.
        * DEPRECATED; see -data_chr_select
        * select only some chr's to be loaded in
        <num1> -- integer, the number of the chr that should be loaded

    -chr_prefix <prefix>
        * DEPRECATED; see -data_chr_prefix
        * changes name of chr to add a prefix string before every chr number
        <prefix> -- string

    -chr_postfix <postfix>
        * DEPRECATED; see -data_chr_postfix
        * changes name of chr to add a postfix string after every chr number
        <postfix> -- string

    -extra_data_col <num1> <num2> etc.
        * DEPRECATED; see -data_metadata_cols
        * designate columns that contain extra data associated with each
          point
        * used to specify a marker # for each point, then when moving the
          cursor, the graph would display what marker # the closest point to
          the mouse curser is at
        <num1> -- integer, the column index

    -chr_same_color <bool>
        * DEPRECATED; use -data_color_per_line instead
        * tells program to either keep all chr's the same color, 
          or to make each chr a different color
        <bool> -- on, off
        * optional, if not present, value is on

    -chr_color_all <color>
        * DEPRECATED; see -data_line_color
        * set the same color for all chrs
        * only works if -chr_same_color is on
        <color> -- color

    -lineset_name <name>
        * DEPRECATED; argument format has changed
        * gives a name to this line set
        <name> -- string, the name of the set

    -missing_values <token1> <token2> ...
        * DEPRECATED; see -data_missing_value_tokens
        * specifies certain values that indicate missing data, if any of
          these values are found in the ppl column, the line will be skipped
        * tokens cannot contain a comma
        * multiple tokens can be specified, separated by spaces
        <token1> -- a number or string of any kind
        * Note: the default character for a missing value is '.'

-title <title>
    * DEPRECATED: see -figure_title and -plot_title
    * sets the title of the figure
    * will appear above the figure
    <title> -- figure title

-title_text_size <size>
    * DEPRECATED; see -figure_title_text_size and -plot_title_text_size
    * indicates a font size for the figure title
    <size> -- Font size, in points. Integer values only. Default is 14.

-lineset_change_name <oldname> <newname>
    * DEPRECATED; see -lineset_name
    * change the name of a line set, changes the name in the legend if the
    legend is set to display line set names 
    <oldname> -- the old name of the line set
    <newname> -- the new name of the line set

-chr_name <oldname> <newname>
    * DEPRECATED; see -line_name
    * change the name of a chr, changes what is displayed at the 
    bottom of the graph
    <oldname> -- the old name of the chr, when chr's are first loaded,
                    their name is simply their chr number, unless a prefix
                    or postfix was applied
    <newname> -- the new name of the chr

-chr_color <name> <color>
    DEPRECATED. Identical to -line_color.

-chr_linestyle <name> <style>
    DEPRECATED. Identical to -line_style.

-chr_thickness <name> <thickness>
    DEPRECATED. Identical to -line_thickness.

-chr_symbol <name> <symbol>
    DEPRECATED. Identical to -line_symbol.

-chr_symbol_size <name> <size>
    DEPRECATED. Identical to -line_symbol_size.

-noshow_chr_names
    * DEPRECATED; see -show_line_names
    * does not show chromosome names in the labels underneath the graph

-ann_use_extra_data <on/off>
    DEPRECATED. Identical to -ann_use_metadata.
-ann_peak_boundaries [plot=<name>] <threshold>
DEPRECATED; see -ann_threshold's peak_boundary mode.
Annotates the boundaries of a peak at a certain threshold.
Specifically, when data points in a line go above the threshold, the first and last data points higher than the threshold are annotated.
[plot=<name>] -- Optional; specifies which plot we're adding annotations to. Can change all plots simultaneously with plot=ALL. (See Special Arguments, above.)
<threshold> -- The threshold value. Real number values only.

...

-overlay_marker_map <file> <chr col> <pos col> <hlines> <size> <color> <symbol> <name> <metadata>
    * DEPRECATED; see -import_markermap_data and the -markerdata_ commands
    * insert gene markers that are specified by a file
    * <file> --> path to file, the file that the gene marker data is in
    * <chr col> --> integer, the column index that specifies what chr this 
      gene marker belongs to
    * <pos col> --> integer, the column that indicates the position of the
                    gene marker
    * <hlines> --> integer, number of header lines
    * <size> --> integer, the size of the markers, default is 4
    * <color> --> color, the color of the markers, default is 'r' (red)
    * <symbol> --> symbol, the symbol used for the markers, default is 'o'
    * <name> --> label, a name given to this set of gene markers
    * <metadata> --> integer, the column with extra data in it
    * every argument after <pos col> is optional, but needs to be in the
      correct order and cannot have any missing parameters. for example, you
      could specify <size> and <color>, but not <size> and <symbol> by
      itself, you would need to specify <size> <color> <symbol>
    * valid symbols are: 'no symbol', 'square', '+', 'o', 'x', 'diamond', 
                         'thin diamond', '^', 'v', '>', '<', '|', '_', 
                         'hexagon', 'pentagon', 'tripod 1', 'tripod 2'
    * can be specified multiple times

-overlap <filename> <pos col> <ppl col> <hlines> <overlap chr>
    * DEPRECATED; see -import_data and -data_overlap
    * reads chromosome information from a file, and overlaps them with
    other chromosomes in the graph
    <filename> -- path to file, the file with the chr data, must be text
                  file
    * <pos col> --> integer, the column index of column with position values
    * <ppl col> --> integer, the column index of column with ppl values
    <hlines> -- integer, the number of header lines
    * <overlap chr> --> label, the name of a current chr in the graph that
                        the overlap will begin at
    * <overlap chr> is optional, if not present, the overlap will begin at
    the first (leftmost) chr

    * all these commands are used to specifiy extra information 
    about the file being opened by -overlap. they should appear
    right after -overlap to ensure that they are assoicated with
    that particular -overlap (just in case there are multiple -overlaps)
    * can be specified multiple times

    -overlap_chr_num <num>
        * DEPRECATED; see -data_chr_num
        * if text file has info about only one chr, tells program what the 
          chr number of that chr is
        <num> -- integer, the number of the chr in the file

    -overlap_chr_col <num>
        * DEPRECATED; see -data_chr_col
        * column index of column with chr number
        * optional, if left out, will assume first set of values is chr1, 
          then second set of values is chr2, etc.

    -overlap_chr_select <num1> <num2> etc.
        * DEPRECATED; see -data_chr_select
        * select only some chr's to be loaded in
        <num1> -- integer, the number of the chr that should be loaded

    -overlap_chr_prefix <prefix>
        * DEPRECATED; see -data_chr_prefix
        * add a prefix string before every chr number
        <prefix> -- string

    -overlap_chr_postfix <postfix>
        * DEPRECATED; see -data_chr_postfix
        * add a postfix string after every chr number
        <postfix> -- string

    -overlap_extra_data_col <num1> <num2> etc.
        * DEPRECATED; see -data_metadata_cols
        * designate columns that contain extra data associated with each
          point
        * used to specify a marker # for each point, then when moving the
          cursor, the graph would display what marker # the closest point to
          the mouse curser is at
        <num1> -- integer, the column index

    -overlap_chr_same_color <bool>
        * DEPRECATED; use -data_line_color instead
        * tells program to either keep all chr's the same color, 
          or to make each chr a different color
        <bool> -- 'on', 'off'
        * optional, if not present, value is 'on'

    -overlap_chr_color_all <color>
        * DEPRECATED; see -data_line_color
        * set the same color for all chrs
        <color> -- color

    -overlap_lineset_name <name>
        * DEPRECATED; see -lineset_name
        * gives a name to this line set
        <name> -- string, the name of the set

* the following 2 commands only apply when -tick_mode is set to 'custom'

-tick_even_multiples
    * DEPRECATED; see -tick_placement
    * always place tick marks at even multiples of the tick interval
    * this is done by default
    * opposite effect of -tick_first_position

-tick_first_position
    * DEPRECATED; see -tick_placement
    * tick marks will always start at the first available position, 
    then be offset by the tick interval amount
    * opposite effect of -tick_even_multiples

-chr_table <rows> <columns> <filename> <chr_list1> <chr_list2> ...
    * DEPRECATED; see -export_collage and the -collage_ commands
    * create a table of individual chromosome graphs and save it as one 
    image
    * <rows> --> number, the number of rows in the table
    * <columns> --> number, the number of columns in the table
    * <filename> --> path to file, the name of the resulting image file.
                     supported formats are .png and .tif
    * <chr_list1> --> a list of chromosome names, each separated by spaces.
    for example, '1 2 3' will specify chromosomes 1, 2, and 3. if the names 
    of chromosomes are numbers, then a range of chromosomes can be specified
    using a dash. for example, '4-12' means chromosomes 4, 5, ..., 12. 
    multiple ranges and lists are separated by spaces.
    * if there are not enough rows or columns to the specified chromosomes,
    the number of rows will be increased until there is enough room
    * can be specified multiple times
    * optional, if left out, will include all chromosomes

    * these commands are used to specifiy extra options with chr_table. 
    * they should appear right after -chr_table to ensure that it is
    assoicated with that particular -chr_table 
      (just in case there are multiple -chr_table commands) 
    * can be specified multiple times

    -chr_table_prevent_tick_overlap_off
        * REMOVED; functionality is being folded into all Kelviz plots
        * usually when making a table of chrosome graphs, a check is done to
          remove any overlapping tick marks. this could cause tick marks at
          uneven intervals, though. specify this option to turn this
          feature off

    -chr_table_custom_legend_position <chr name> - <legend position>, ...
        * DEPRECATED; see -collage_legend_location
        * normally the legend position is the same for every graph in a
          table of individual chromosome graphs. use this option when you
          want the legend to be in different positions for different
          chromosome graphs
        * <chr name> --> the name of a chromosome
        * <legend position> --> the position of the legend
          possible values include: 'upper right' , 'upper left',
                                   'upper center', 'lower right',
                                   'lower left', 'lower center', 
                                   'center left', 'center right', 'right', 
                                   'center'
        * note that a dash is used to separate the chromosome name from the
          legend position
        * multiple chromosomes can be specified. just list each name/legend
          position pair one after another, seperated by a comma
          (example: '1 - upper right, 2 - lower left, 3 - center') 
        * if a chromosome that is listed to be in the table is not listed to
          have a custom legend position, then the normal legend location is
          used (as set by -legend_location)

    -chr_table_separate_legend_position
        * DEPRECATED; see -collage_separate_legend
        * normally every graph in a table has its own legend. use this
          option when you want only one legend for every graph

    -chr_table_one_title
        * REMOVED; see `-collage_autotitles` and `-collage_title`
        * normally every graph in a table has a title. use this option when
          you want there to be only one title at the top of the image.

-lineset_table <rows> <columns> <filename> <lineset1>, <lineset2> ...
    * DEPRECATED; see -export_collage and the -collage_ commands
    * create a table of individual line set graphs and save it as one image
    * <rows> --> number, the number of rows in the table
    * <columns> --> number, the number of columns in the table
    * <filename> --> path to file, the name of the resulting image file.
                     supported formats are .png and .tif
    * <lineset> --> name of a lineset, multiple lineset names can be
                    specified, separated by commas
    * if there are not enough rows or columns to the specified line sets,
    the number of rows will be increased until there is enough room
    * can be specified multiple times
    * optional, if left out, will include all linesets

    * these commands are used to specifiy extra options with lineset_table
    * they should appear right after -lineset_table to ensure that it is
      assoicated with that particular -lineset_table 
      (just in case there are multiple -lineset_table commands) 
    * can be specified multiple times

    -lineset_table_prevent_tick_overlap_off
        * REMOVED; functionality is being folded into all Kelviz plots
        * usually when making a table of line set graphs, a check is done to
          remove any overlapping tick marks. this could cause tick marks at
          uneven intervals, though. specify this option to turn this
          feature off

    -lineset_table_custom_legend_position <lineset name> - <legend position>,...
        * DEPRECATED; see -collage_legend_location
        * normally the legend position is the same for every graph in a
          table of individual line set graphs. use this option when you
          want the legend to be in different positions for different line
          set graphs
        * <lineset name> --> the name of a line set
        * <legend position> --> the position of the legend
          possible values include: 'upper right' , 'upper left',
                                   'upper center', 'lower right',
                                   'lower left', 'lower center', 
                                   'center left', 'center right', 'right', 
                                   'center'
        * note that a dash is used to separate the line set name from the
          legend position
        * multiple line sets can be specified. just list each 
          line set/legend position pair one after another, seperated by a
          comma
          (example: `lineset1 - upper right, lineset2 - left`) 
        * if a line set that is listed to be in the table is not listed to
          have a custom legend position, then the normal legend location is
          used (as set by -legend_location)

    -lineset_table_one_title
        * REMOVED; see `-collage_autotitles` and `-collage_title`
        * normally every graph in a table has a title. use this option when
          you want there to be only one title at the top of the image.
-collage_prevent_tick_overlap <on/off>
REMOVED; functionality is being folded into all Kelviz plots
Indicates whether or not we want to make sure tick marks don't overlap.
By default, when making a collage, a check is done to remove any overlapping tick marks. This can potentially cause tick marks to appear at uneven intervals, though, and so it is optional.
<on/off> -- Turn this option ON or OFF. Defaults to ON.
-collage_one_title <on/off>
REMOVED; see -collage_autotitles and -collage_title
Toggles whether or not we want one title for all subplots (the default) or if we want each subplot to have its own copy of the title.
<on/off> -- Turn this option ON or OFF. Defaults to ON.