User Guide
PGGpopulation.org provides researchers with convenient online tools that could generate journal-level visualizations of analysis results. The built-in processing tools allow users to upload their own populations of interest, and by uploading files they could easily.
We currently provide three interactive data visualizing tools: Principle Component Analysis (PCA), ADMIXTURE and FST. All tools have data view, refresh and download figure functions, which can be found at the upright corner of each tool.
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PCA:
The PCA plotting tool is an interactive plot that could extract two dimensions of PCA analysis (Default PC1 and PC2), and the percentage of each principle component is shown on axis labels. Each point presents a population, while their colors are defined by their classes. Hovering on the points will trigger a small window containing full information for this population.
ploading file format:

Individual ID: The unique id for each individual in the group. Defined by users.
PC1…PC10: The principle component values for each individual. Uploading files should contain all 10 PCs.
Population name: The name of each population. Defined by users.
Classes (not necessary): Classes of populations based on their geographical or ancestry information. If not set, all populations will be set as class 1.

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ADMIXTURE:
The ADMIXTURE plotting tool allows users to visualize their own ADMIXTURE result. Each line represents one individual, with the colors on it represents the proportion of each component in ADMIXTURE analysis. Hovering on the lines will trigger a small window showing the details of the individuals. The number of ancestries (k) covered in the analysis can be set by clicking the colored rectangles to disable/enable a specific ancestry. Mouse wheel spinning on the plot will zoom in/out the plot, allowing the users to generate a broader or more detailed plot.
Uploading file format:
The tool supports the original ADMIXTURE output file format, which is shown below:

ID: Default ADMITURE output number.
Individual ID: User-defined id for each individual.
Population name: User-defined population name.
k1…k20: The output values of ADMIXTURE. The limitation for k numbers is 20.

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FST:
The FST tool provides an interactive visualization of comparisons between one specific group and other groups. The populations can be set into different classes for separated comparisons. Hovering on the lines will trigger a small window containing the information for the current population.

Uploading file format:

Population 1: The reference population in comparison. WARNING: the uploading file should only contain 1 population 1.
Population 2: The population for comparison with population 1.
FST: The FST value of comparisons.
Classes (not necessary): Classes of populations based on their geographical or ancestry information. If not set, all populations will be set as class 1.