DArTView¶

DArTView is a KDXplore plugin for marker data curation via metadata filtering. DArTView enables users to overcome the tedious manual calculation of marker data that is common when using spreadsheet applications. You may do this with the following steps:

Creating a formula for a statistic (e.g. Marker Call Rate);
Extending the formula to the entire dataset;
Sorting data via calculated statistics;
Visualising calculated statistics (e.g. via scatter plot);
Subsetting dataset based on the determined threshold; and
Repeating steps 1-4 to look at the effect on other statistical distributions.

This user guide provides an overview of DArTView, as well as functions such as those listed above. If you would like access to DArTView, then see the KDXplore Getting Started page.

Note

If you experience any issues or have feedback, don’t hesitate to get in touch with us at kdxplore@diversityarrays.com

Supported Formats¶

DArTView supports multiple nucleotide genotypic data types of DArT and HapMap marker data formats:

DArT

DArT Counts

DArT SNP Two Row

DArT Silico SNP

DArT Silico Counts

DArT SNP One Row

HapMap

Two Letter

SSR

Codominant

Dominant

Note

These formats will be referred to as marker data throughout this user guide.

DArTView Main Window¶

The DArTView Main window displays an opened file and filters and graphs that you have applied. See the below image and table for more information about the sections of the DArTView Main window:

Panels of the DArTView Main Window¶
Item	UI Element	Description
	Metadata Panel	Lists metadata that is organised into markers/samples, each with numeric/non-numeric subsections. Checked metadata are displayed as graphs in the Graphs panel.
	Filters Panel	Lists all active/inactive filters added to the file and provides options for managing these filters.
	Graphs Panel	Displays scatter, and histogram plots based on the filters applied to a file.

Viewing Metadata Statistics¶

Data can be viewed after it is loaded from a marker data file. The options for viewing data are outlined in the image and table below:

Viewing Data¶
Item	UI Element	Description
	Report Counts	The total number of markers and samples are displayed here.
	Metadata Tabs	Select either the Markers tab or the Samples tab to view the report’s metadata on markers or samples. The Numeric tab and Non-Numeric tab allows the user to view numeric and non-numeric metadata.
	Stats Button	The Metadata panel in the above image displays only basic metadata stats. Select the Stats button to choose the all stats option which shows all metadata stats available.
	Genotypic Data Map button	This button will open a window called the Genotypic Data map, where you can graph data. See the section below for more information.
	Metadata Panel	This panel displays metadata according to what tabs the user has selected to view. Select the checkbox or double-click on any of the rows to display further information on the metadata. This is demonstrated in the image below, where the callrate is selected and displayed.

Metadata Statistics¶

DArTView provides both numeric and non-numeric summary statistics for marker data files. The below tables lists these statistics and provides descriptions for each one:

Numeric Summary Statistics¶
Statistic	Description
Min	The minimum value for this metadata statistic.
Mean	The mean value for this metadata statistic.
Max	The maximum value for this metadata statistic.
Extended: Q1	First interquartile range. The middle value in the first half of the rank-order data set.
Extended: Median	Second interquartile range. The middle value of the rank-order data set.
Extended: Q3	Third interquartile range. The middle value in the second half of the rank-order data set.
Extended: Variance	The sample variance of the statistic: \(\frac{1}{N-1}\sum_i^N (\overline{X} - X_i)^2\)
Extended: Std Dev	The sample standard deviation of the statistic: \(\sqrt{\frac{1}{N-1}\sum_i^N (\overline{X} - X_i)^2}\)
Extended: Std Err	The sample standard deviation of the statistic: \(\frac{\sqrt{\frac{1}{N-1}\sum_i^N (\overline{X} - X_i)^2}}{\sqrt{N}}\)

Non-Numeric Summary Statistics¶
Statistic	Description
Values	Displays some entries of the metadata

Metadata Source Types¶
Source	Description
Calculated	Metadata has been calculated using DArTView’s internal set of calculators for this data format.
Report	Metadata was imported from a report.
Imported	Metadata was imported via Import Metadata wizard.

Viewing Graphed Metadata¶

You can view each metadata row in more detail in different graphs located in the Graphs panel. Select the checkbox or double-click on any of the rows to display more information in scatter plots and histograms of the data.

The images below are examples of the callrate being graphed as both a scatter plot and a histogram. The data is displayed in descending order as that is what order it was designated in the Metadata panel. There are also checkboxes along the bottom of the scatter plot, which provide options for marking summary statistics of the data. The median is marked in this example and can be seen with the blue line through the scatter plot.