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Using the Graph Control Interface

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12.5 Using the Graph Control Interface

The Graph Control Interface has three components, User Graphs, Annotation Tracks, and the Graph and Item settings control boxes.

In general, the node structure consists of User Graphs as the top level node (trunk) where any and all graphs that the user creates are placed under this node, and where new graphs can be created. Next in the hierarchy are Graphs, which are the parent nodes (or branches) and Items are the child nodes (or leaves). If a Graph is selected then the Graph Controls will be visible at the bottom of the Graph Control Interface, but if a graph item is selected then the Item Controls will be visible.

The Annotation Tracks top-level node is described in Features Unique to a Genome Browser.

Using the User Graphs Tree Window

[Picture]

Figure 93: Two XY Scatter Plots in a Plot Viewer–Graph Item Filter Tab Visible

The Tree Structure

The User Graphs Tree displays the structure of all graphs and items in each graph. (See Figure 93 the Graph Control Interface is in the black box.) The top levels of the tree correspond to different graphs in the Graph View. From a particular graph, all items in the list under each graph name are the Items. An Item is a column of data or line plotted in a graph. The order of the Items dictates the order in which the points are drawn in the graph. The Item on the top of the list of Items for a graph will be plotted on top of all other graph items. To have an Item on top of all other points in the graph, left-click on the Graph Item name and drag and drop the Graph Item directly below the graph name. In the case of LD plots, an item is the Haplotype Blocks, no other items can be added to LD plots.

To save space, the tree structure for a particular graph can be minimized by clicking the symbol to the left of the graph name hiding the graph. To reshow all graph items, click on the symbol to the left of the graph name. Minimizing a graph in the tree will not change what is displayed in the Graph Viewer.

Add a New Graph

To add a new graph click on the User Graph Tree, this causes the Add Graph to become available in the control panel.

There are two cases of what this control panel looks like, depending on if the X-axis is in the genomic position scale or not. These cases are detailed below.   Not in genomic position scale  The search filter allows the user to search among the column name headers for all numeric columns (real-valued (R),integer-valued (I), or binary (B)) from the spreadsheet that created the Plot Viewer. The R/I/B toggle buttons can be deselected or selected to hide or show columns of the specified type. The filter searches all columns of the specified type(s) for the occurrence of the entered string in any part of all column name headers, not necessarily at the beginning of the name. For example, entering the letter “a” in the text box will display up to 1,000 column name headers with “a” anywhere in the header string. Only 1,000 column name headers are listed at once to maintain the speed and usability of the list.
Columns cannot be added from other spreadsheets.
  In genomic position scale  Columns from row marker mapped spreadsheets can be added to the plot viewer in addition to columns from the originating spreadsheet. Heat Maps and LD plots can also be added from column marker mapped spreadsheets containing at least two marker mapped columns of numeric (Real, Integer or Binary) or genotypic data respectively.
To select a spreadsheet other than the originating spreadsheet or currently selected spreadsheet, click on the Spreadsheet Button. Then select Select Spreadsheet.... All marker mapped spreadsheets in the project are listed in the spreadsheet selection dialog. After selecting a spreadsheet, click OK. The columns/graphs available for plotting from the selected spreadsheet will be listed in the column selection box. If a spreadsheet with a long name is selected, part of the name will not be visible on the Spreadsheet Button, but a tool tip with the full spreadsheet name is available after hovering over the button or spreadsheet name in the list box.
The search filter allows the user to search among the column name headers for all numeric columns (real-valued (R),integer-valued (I), or binary (B)) from the selected spreadsheet. The R/I/B toggle buttons can be deselected or selected to hide or show columns of the specified type. The filter searches all columns of the specified type(s) for the occurrence of the entered string in any part of all column name headers, not necessarily at the beginning of the name. For example, entering the letter “a” in the text box will display up to 1,000 column name headers with “a” anywhere in the header string. Only 1,000 column name headers are listed at once to maintain the speed and usability of the list.
All columns listed in the column selection box can be selected by clicking on the All button.
The selection of columns can be cleared by clicking on the Clear button.
Once one or more columns are selected they can be added to the plot viewer by clicking the Add button. NOTE: Selection of multiple columns between multiple spreadsheets is not allowed for a simultaneous add.

Hide a Graph

A graph can be hidden from view without removing its configuration settings. To do this, un-check the box in front of the graph name. This does not remove the graph or its settings from the Plot Viewer, but does remove it from the Graph View. To re-show the graph, check the box in front of the graph’s name.

Rename a Graph Title

To rename a graph, right-click on the graph name and select “Rename”. Renaming the graph node will change the title of the graph, which is displayed when the “Title” option is checked. (See Features Unique to a Genome Browser.)

Reordering Graphs

Graphs can be reordered within the User Graphs tree, preserving all Graph settings. To reorder a graph, click on the graph and drag it to the desired location. The effect of reordering graphs in the User Graphs Tree is that the graph is placed below the location where it is dropped.
Multi-select operations are valid for moving graphs. These are: <Ctrl>-left-click selects multiple graphs one at a time, and <Shift>-left-click selects all graphs between the first and last selected graph or item. All selected graphs will be moved to below the specified location from bottom to top of the list of graphs moved.

Delete an Entire Graph

To delete a graph and its associated graph items and remove all its associated settings from the Plot Viewer, right-click on the graph name and select “Delete”.
Multi-select operations are valid for deleting graphs. These are: <Ctrl>-left-click selects multiple graphs one at a time, and <Shift>-left-click selects all graphs between the first and last selected graph or item. All selected graphs will be deleted.

Hide an Item

To hide or prevent drawing of a graph, un-check the box in front of the graph item name. This does not remove the graph item or its settings from the Plot Viewer, but does remove it from the Graph View. To re-show the graph item, check the box in front of the graph item name.

Rename an Item

To rename a graph item, right-click on the graph item name and select “Rename”. Renaming the graph item will also change the name displayed in the legend.

Reordering or Moving Items

Graph Items can be reordered within a graph or moved from one graph to another, preserving all Item settings. To move or reorder an item, click on the item and drag it to the desired location. The effect of reordering items for a graph in the User Graphs Tree is that the item layers are reordered.
Multi-select operations are valid for moving items. These are: <Ctrl>-left-click selects multiple items one at a time, and <Shift>-left-click selects all items between the first item and last selected graph or item. All selected items will be moved to below the specified location. The item that was at the bottom of the item list before selection will be the last item added.

Delete an Item

To delete an item from a graph (which will remove all of its settings from the the Plot Viewer), right-click on the graph item and select “Delete”.
If an item or graph is deleted by mistake, closing the SVS project without saving changes and reopening will revert the project to the last saved state.
Multi-select operations are valid for deleting items. These are: <Ctrl>-left-click selects multiple items one at a time, and <Shift>-left-click selects all items between the first item and last selected graph or item. All selected items will be deleted.

Graph and Item Controls

There are different options and settings for graphs and items. To set the options for a graph, click on the name of the graph for which the settings are to be changed. To set the options for an item, click on the name of that graph item. The options and settings that can be changed for Graphs and Items are listed below.

Multi-select operations are valid for editing graphs or items. These are: <Ctrl>-left-click selects multiple graphs or items one at a time, and <Shift>-left-click selects all graphs or items (of the same type as the first selection) between the first and last selected graph or item. Any options set for all selected graphs or items will be applied to all selected graphs or items.

Graph Controls

Graph controls dictate the general structure of the graph, axes, title, legend, domain and range, if a chromosome shader should be used (if applicable), and the addition of any graph items to the graph.

The graph controls are displayed on two tabs. These tabs and their options are displayed below.

  • Graph:
    • Title: Check this box to display the graph title (all plot types).
    • Vertical Flip: Flips an LD plot vertically (only available for LD plots).
    • Overlay: Color for the overlay grid (only available for LD plots).
    • Legend: Check this box to display the graph legend (all plot types except LD).
    • Chromosome Shader: Check this box to shade chromosomes in the Graph Viewer. (Only available for numeric plots including LD and Heat Maps with genetic position for the X-axis.)
    • Bin Count Sets the global number of bins for the entire graph. The bins are calculated by taking the minimum and maximum values over all items and subdividing this range by the number of bins specified. (Only available for Histograms.)
    • Region: Specify the region for the X-axis to span in this box. (Only available for numeric plots including LD and Heat Maps with genetic position for the X-axis.) Examples of formats for the region box are:
      • “chr#”
      • “chr#:StartPos-EndPos”
      • “chr#:StartPos-chr#:EndPos”
      • “chr#-chr#”

      You can right-click to copy and paste this region string in a document or in a specific genome browser.

    • Row-Min and Row-Max: Specifies the start position row number and the end position row number for zooming in on the X-axis. (Only available for Numeric Value Plots without a marker map applied to the row labels.)
    • X-Min and X-Max: Specifies the minimum and maximum X-axis values for setting the domain of the plot. (Only available for Histograms or XY Scatter Plots.)
    • Y-Min and Y-Max: Specifies the minimum and maximum Y-axis values for setting the range of the plot. (All plot types except LD.)
    • Marker color: Sets the marker flag color (only available on LD plots.)
    • Data Aggregation Method: Sets the data aggregation method for Heat Maps, choices are color pixels based on the Mean, Min, Max or Extreme value (only available for Heat Maps).
  • Axes:
    • X-Label: Check this box to display the specified X-label (all plot types).
      • Axis: Check this box to display the X-axis. If this box is unchecked then the grid will not be displayed for the x-axis as well (all plot types).
      • Grid: Check this box to display the grid for the X-axis (all plot types).
    • Y-Label: Check this box to display the specified Y-label (all plot types, note label cannot be changed for LD).
      • Axis: Check this box to display the Y-axis (all plot types).
      • Grid: Check this box to display the grid for the Y-axis (all plot types except LD).
  • Add Item: Contains a list of up to the first 1000 few numeric columns in the spreadsheet as well as a line item “f(x) = m(x) + b”. Checking the box in front of any of these items in the list will create a new graph item in the graph. The settings for these items can be set after adding them to the graph. The search filter can be used to easily select columns by entering a search string. Deselecting or selecting the column type toggle buttons can also help to restrict which columns are shown or searched.

    For numeric plots including LD and Heat Maps with genetic position for the X-axis, items can be added from other marker mapped spreadsheets. To select a spreadsheet, click on the Spreadsheet Button.

  • Color (LD Plots): Additional colors can be added or removed from the LD intensity scale. Colors can also be changed by clicking on the color buttons. The value for setting the colors can be changed by double clicking on the value.
  • Method Options: (Only available for LD)
    • Method: The method consists of two parts, the method and the statistic, the first menu is the method (EM or CHM) and the second is the statistic (R2 or D′)
    • Options for EM Method: (Only available when EM method is selected.)
      • Use samples with missings: Indicates whether samples with missing values should be used for the computation.
      • Max Iterations: The maximum number of iterations used for EM computation.
      • Conv Tolerance: Convergence Tolerance for EM method computation.
  • Color (Heat Maps): (Only available for Heat Maps)
    • 2 Color Auto: The minimum and maximum values are calculated for the data visible in the graph. Only the colors can be changed in this mode.
    • 3 Color Auto: The minimum, mean and maximum values are calculated for the data visible in the graph. Only the colors can be changed in this mode.
    • Manual: Additional colors can be added or removed and the values for setting the colors can be changed. CNV Default settings can be selected. The values for the colors can be changed after selecting this option.

Item Controls

The Item Controls are displayed on up to three tabs. These tabs and their options are displayed below.

NOTE: Heat Maps and Annotation Tracks do not have items associated with them and are excluded from the designation of “all plots” for this section.

  • Item: All plots, except histograms and LD, contain the following options and settings:
    • Line: options include the line style, color and weight. If “No Line” is selected from the line type list box, then the other options are grayed out. The line types include:
      • No Line – no line connects the points.
      • Solid – a solid line connects the points to one another.
      • Drop – a line connects the points to the X-axis.
      • Steps – a line connects the points to one another by first stepping up or down and then over to the location of the next point.

      To change the color of a line, select a line, click on the color button and select the desired color. To change the weight of the line, increase or decrease the number in the list box.

    • Symbol: options include the symbol and the color and size of the symbol. If “None” is selected from the symbol list box then the other options are grayed out. There are several different options for symbols. To change the color of a symbol, select a symbol, click on the color button and select the desired color. To change the size of the symbol, increase or decrease the number in the list box.
  • Item: Only Histograms contain the following options and settings:
    • Outline: color selector sets the outline color of the histogram bars, and for the median/mean lines.
    • Fill: color selector sets the fill color of the histogram bars.
    • Opacity: sets the opacity of the histogram. When the slider is all the way to the left, the histogram is completely transparent, all the way to the right and it is completely opaque. Adjusting the opacity is useful when more than one histogram is displayed in a graph and the two histograms overlap.
    • Median: Checking this box shows a line representing the median of the values for the column plotted in the histogram. The color of this line is determined by the outline color.
    • Mean: Checking this box shows a line representing the mean of the values for the column plotted in the histogram. The color of this line is determined by the outline color.
  • Item: Only LD contain the following options and settings:
    • Block Definitions:
      • Load...: Load pre-computed block definitions.
      • Save: Save user defined block definitions to a spreadsheet for later use.
      • Clear All: Clear all blocks from the LD plot.
      • Compute...: Compute haplotype blocks.
    • Tables for Block #: Available if a haplotype block is selected.
      • Haplotype Tables: Outputs various haplotype tables.
      • Subset Markers: Creates a subset spreadsheet based on the markers in a haplotype block.
    • Console Output Option: sets the threshold for displaying haplotypes in the Data Console.
  • Smoothing: All plots, except histograms and LD, contains the following options and settings: Smoothing replaces the Y coordinates with a smoothed valued based on the specified window. The smoothing options are:
    • Mean Smooth, Symmetric
    • Median Smooth, Symmetric
    • Mean Smooth, Asymmetric
    • Median Smooth, Asymmetric

    The window radius value specified for the window indicates the number of points to use for smoothing on either side of the point being smoothed. For example, a window value of 2 replaces each point with a 5 point median or mean value.

    The difference between Symmetric and Asymmetric smoothing is how the boundary cases are handled.

  • Filter: All plots (except for LD) contain options and settings for plotting filtered values or plotting the values with different colors based on a split criteria. Filtering edits the graph item name and the values displayed in the graph view. As soon as a column to be used for filtering and the filter criteria has been specified, only those values matching the criteria will be displayed. These options and settings are:
    • Search: Allows column headers to be filtered on the specified search criteria. Column type toggle buttons B/I/R/C/G can be deselected/selected to restrict which column types are shown in the column chooser.
    • Column Chooser: Lists up to the first 1,000 columns in a spreadsheet that could be used for filtering or splitting. Selecting a numeric valued column (except binary) allows filtering or splitting based on a threshold. Selecting a categorical, genotypic or binary column allows for filtering or splitting based on certain categories or values.
    • Split: creates a new graph item for every category or complementary filter criteria (i.e. a graph item for <= and one for >).
    • Numeric Filter Criteria: displays numeric filtering criteria if the column used for filtering is real- or integer-valued.
    • Numeric Threshold Value: allows for input of the numeric value used for specifying the threshold for filtering or splitting.
    • Categorical Selection: displays all possible categories that could be used for filtering based on the categories of the categorical, genotypic or binary column used for filtering. The category you choose will be the only category displayed in the graph.
    • Clear Filter: clears the filter and displays all values for the graph item.
Adding a Line to a Graph

To add a line (other than a vertical line) to a graph, select the graph and in the Graph Options select the Add Item tab. From this tab check the box in front of the f(x) = m(x) + b item in the list box and click Add. This will add by default the line f(x) = x to the graph.

The slope and intercept of the line can be changed by clicking on the graph item created after the line was added. This graph item has only one Graph Item control tab, the Attributes tab. On this tab there are the following controls:

  • Line: Set the color and weight of the line.
  • Slope: Set the slope of the line.
  • Intercept: Set the Y-intercept of the line.

The graph item name will be changed to reflect the current equation of the line, but this graph item can also be renamed by right-clicking on the current graph item name and selecting “Rename”.

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