‹‹ Back to SVS Home

Opening the Plot Viewer

[next] [prev] [prev-tail] [tail] [up]

11.4 Opening the Plot Viewer

There are several ways to open the Plot Viewer. Two of which, via the Plot menu or the Tool Bar, open a Parameters dialog to set up the initial parameters for the graphs and plots in the Plot Viewer. The third way, via the column header menu, is a short cut to be used when the user knows exactly which column is to be plotted (or in the case of the XY Scatter Plot, which column is the dependent and which is the independent column). The third approach is most useful when only one graph is desired. Each is described below.

From the Plot Menu

The plot parameters dialog for each of the three types of plots with this dialog can be opened using the Plot menu. Linkage Disequilibrium (LD) and Heat Map plots can be opened directly from the Plot menu, these plots do not have a parameters dialog.

Plot Numeric Values

To plot numeric values against the row label or genetic position, select Plot > Plot Numeric Values (see Figure 88).

[Picture]

Figure 88: Numeric Value Plot Parameters Window

The Numeric Value Plot Parameters dialog allows for the selection of multiple Numeric Value Plots to be plotted simultaneously in the same Plot Viewer as the dependent Y-axis and for the initial plot parameters to be set.

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)). 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 “-22” in the text box will display up to 1,000 column name headers with “-22” anywhere in the header string. Only 1,000 column name headers are listed at once to maintain the speed and usability of the list.

If there are a small number of columns in the list box either before or after filtering, all columns can be selected by clicking All. All selections can be cleared by clicking Clear.

The item arrangement can also be specified. The choices are:

  • Plot one item per graph
  • Plot all items in one graph

To plot the selected columns with the selected item arrangement, click Plot, to cancel the plot click Cancel.

Plot Histograms

To plot one or more histograms, select Plot > Histograms (see Figure 89).

[Picture]

Figure 89: Histogram Parameters Window

The Histogram Parameters dialog allows for the selection of multiple numeric columns to be plotted simultaneously as histograms in the same Plot Viewer.

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)). 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.

If there are a small number of columns in the list box either before or after filtering, all columns can be selected by clicking All. All selections can be cleared by clicking Clear.

The item arrangement can also be specified. The choices are:

  • Plot one item per graph
  • Plot all items in one graph

To plot the selected columns with the selected item arrangement, click Plot, to cancel the plot click Cancel.

Plot XY Scatter Plots

To plot one or more XY Scatter Plots using the same independent variable (X-axis), select Plot > XY Scatter Plots (see Figure 90).

[Picture]

Figure 90: XY Scatter Parameters Window

The XY Scatter Parameters dialog allows for the selection of multiple numeric columns to be plotted simultaneously against one independent variable (or X-axis) as scatter plots in the same Plot Viewer.

This dialog has two search filters, one for the selection of the independent (X-axis) variable, and the other for the selection of one or more dependent (Y-axis) variables. Each 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)). The R/I/B toggle buttons can be deselected or selected to hide or show columns of the specified type. The filter searches for the occurrence of the entered string in any part of all column name headers for the specified column type(s), 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 of columns.

If there are a small number of columns in the list box for the selection of the dependent variable, either before or after filtering, all columns can be selected by clicking All. All selections can be cleared by clicking Clear.

The item arrangement can also be specified. The choices are:

  • Plot one item per graph
  • Plot all items in one graph

To plot the selected columns with the selected item arrangement, click Plot. To cancel the plot click Cancel.

Plot Linkage Disequilibrium

To plot Linkage Disequilibrium (LD) based on the genotypes in the current spreadsheet, select Plot > Linkage Disequilibrium.

Plot a Heat Map

To plot a Heat Map based on all active rows and columns, select Plot > Heat Map.

From the Tool Bar

Each of the three plot parameter dialogs (Numeric Value, Histogram, XY Scatter Plot) can be opened by selecting the appropriate plot icon in the Spreadsheet Viewer Tool Bar. LD and Heat Maps can be created directly by selecting the corresponding icon. Holding the mouse over one of the plot icons will display a tooltip message indicating the plot type. See From the Plot Menu for more information on the five plot types and their parameter dialogs if one exists.

From a Column Header Menu

If a particular column is to be plotted as either a Numeric Value Plot or a Histogram, clicking on the Column Number Header or right-clicking on the Column Name Header will display the Column Header Menu. To plot the column as a Numeric Value Plot, select Plot Variable. To plot the column as a Histogram, select Plot Histogram. Either one of these options will directly open up the Plot Viewer with default plot options.

In order to plot a XY Scatter Plot from the column header menu, at least one column state must be set to dependent. (See Column States for more information on setting column state).

NOTE:

  • Using this method could create another navigator window node because the state of one or more columns might be changed. Once a column is set as dependent this column will become the Y-axis.

Click on the Column Number Header or right-click on the Column Name Header to get the Column Header Menu for the column that is to be used as the independent variable (X-axis). The XY Scatter Plot option will indicate that the current column will be set as the X-axis. So to plot the one or more dependent columns against this column in XY Scatter Plots, select Plot X:[Column Name Header] vs Y:Dependent(s)

[next] [prev] [prev-tail] [front] [up]