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Types of Plots Available

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11.1 Types of Plots Available

There are five major plot types available in SVS. These include Numeric Value Plots, Histograms, and XY Scatter Plots, Linkage Disequilibrium and Heat Maps. If a Numeric Value Plot is created from a marker mapped spreadsheet where the rows are marker names, then the plot will represent a Genome Browser. A Genome Browser consists of a graph or graphs plotted on a genomic position scale and Annotation Tracks. A heat map can be generated from a spreadsheet with an applied marker map regardless of the orientation of the marker map; the markers will in either case be along the X-axis. All plots except LD are created using numeric data columns within a spreadsheet. LD is created using genotypic columns within a spreadsheet. These plot types are described below.

Numeric Value Plots

The Numeric Value Plot is a plot of the row label on the X-axis and the value from the column plotted on the Y-axis. Unless a marker map is applied to the row labels, sorting the spreadsheet by a column will result in changing the order the data values are plotted in.

The Numeric Value Plot is used to look for trends associated with a row label or the values for one column. The typical p-value plot (either in the natural scale or in the −log 10 scale is a Numeric Value Plot).

Histograms

The Histogram is a plot of the frequency of the values in the column plotted. The X-axis is the range of values in the column, and the Y-axis is the frequency of the observations. The number of bins used in the histogram can be changed. Fewer bins will result in higher frequency counts per bin. More bins will result in smaller frequency counts per bin.

The Histogram is used to look for the shape of the distribution of the values in the column plotted.

XY Scatter Plots

The XY Scatter Plot is a plot of one column as an independent variable against one or more columns as dependent variables. The independent variable used for the X-axis and the dependent variable(s) is/are used to define the Y-axis.

The XY Scatter Plot is used to look for relationships between two or more variables.

LD Plots

The LD plot is a triangular heat map of the LD statistics (D′, R2) between pairs of markers across the genome. The X-axis consists of the active markers from the source spreadsheet. If the markers have a marker map applied they will be spaced proportionally to their map’s position information. Otherwise they will be evenly spaced.

If a binary dependent variable is selected, some basic association statistics will be displayed in the Data Console when you specific LD points are selected in the graph. Blocks of markers can be created, edited and investigated in a LD plot.

The LD Plot is used to investigate areas of the genome in strong LD. See Using LD Plots for more information.

Heat Maps

A Heat Map is an intensity plot of numeric values from a spreadsheet. The X-axis consists of the active markers or columns from the source spreadsheet. The Y-axis consists of sample indices where the ith index corresponds to the ith active sample.

If either the column headers or row labels are genetic markers and have a marker map applied the markers will be placed along the X-axis (regardless of the orientation in the spreadsheet), and will be spaced proportionally to their map’s position information. Otherwise they will be evenly spaced and the orientation will be identical to the orientation in the spreadsheet.

A Heat Map is used to investigate areas of the genome with patterns of loss or gain for multiple samples. See Heat Maps for more information.

Genome Browser

If a genetic marker map is applied in the necessary orientation of a spreadsheet for the specified plot type, the genomic information is used to plot the data points according to chromosome and genetic position. The acceptable marker map orientations are:

  • Markers are in Rows:
    • Numeric Value Plots
    • Heat Maps
  • Markers are in Columns:
    • Heat Maps
    • Linkage Disequilbrium

Additional annotation tracks are also displayed at the bottom of the Plot Viewer in this case. Alternate chromosomes are shaded in the Full Domain View to illustrate chromosomal boundaries.

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