DArTView¶
DArTView is a KDXplore plugin for marker data curation via metadata filtering. DArTView enables users to overcome tedious manual calculation of marker data that is common when using spreadsheet applications. This may be done 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 14 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, please contact 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, as well as filters and graphs that have been applied. See the below image and table for more information about the sections of the DArTView Main window:
Item 
UI Element 
Description 

Metadata Panel 
Lists metadata that is organised into markers/samples with subsections numeric/nonnumeric each. Checked metadata are displayed as a graphs in the Graphs panel. 

Filters Panel 
Lists all active/inactive filters that have been added to the file and provides options for managing these filters. 

Graphs Panel 
Displays scatter and histograms 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:
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 metadata on markers or samples from the report. The Numeric tab and NonNumeric tab allows the user to view numeric and nonnumeric 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 displays all metadata stats available. 

Genotypic Data Map button 
This button will open a window called the Genotypic Data map where data can be graphed. 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 doubleclick 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 nonnumeric summary statistics for marker data files. The below tables lists these statistics and provides descriptions for each one:
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 rankorder data set. 
Extended: Median 
Second interquartile range. The middle value of the rankorder data set. 
Extended: Q3 
Third interquartile range. The middle value in the second half of the rankorder data set. 
Extended: Variance 
The sample variance of the statistic: \(\frac{1}{N1}\sum_i^N (\overline{X}  X_i)^2\) 
Extended: Std Dev 
The sample standard deviation of the statistic: \(\sqrt{\frac{1}{N1}\sum_i^N (\overline{X}  X_i)^2}\) 
Extended: Std Err 
The sample standard deviation of the statistic: \(\frac{\sqrt{\frac{1}{N1}\sum_i^N (\overline{X}  X_i)^2}}{\sqrt{N}}\) 
Statistic 
Description 

Values 
Displays some entries of the metadata 
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¶
Each metadata row can be viewed in more detail in different graphs located in the Graphs panel. Select the checkbox or doubleclick on any of the rows to display more information in the form of 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.