## Introduction

This article describes how to produce a 2-dimensional scatterplot to visualize either high dimensional numeric data or a distance matrix.

## Requirements

- High dimension variables in your data set, or
- A distance matrix

## Method 1: Using Variables

1. From the toolbar menu, select **Anything > Advanced Analysis > Dimension Reduction > Dimension Reduction Scatterplot. **

2. Select one of the available dimension reduction techniques from the **Algorithm** input:

- Principal Component Analysis
- t-SNE
- MDS - Metric
- MDF - Non-metric

3. Select your input variables from the **Variables** drop-down list.

4. OPTIONAL: Tick the **Normalize variables** checkbox to normalize the data:

- For
*t-SNE*and*MDS*each variable is standardized to the range [0, 1] - For
*PCA*the correlation matrix is used rather than the covariance matrix

5. OPTIONAL: When **Create binary variable from categories** is checked, unordered categorical variables with N categories are converted into N-1 binary indicator variables. Otherwise such variables are each converted to a single numeric variable with integers representing categories (as happens for ordered categories).

6. OPTIONAL: Enter a value for **Perplexity** which is a parameter used by the *t-SNE* algorithm and related to the number of nearest neighbors considered when placing each data point. The typical useful range is from 5 to 50 and the default value is 10.

- Low values imply that immediately local structure is most important.
- High values increase the impact of more distant neighbors and global structure

7. Select a **Group variable** to categorize the output. If numeric, the data are shaded from light (lowest values) to dark (highest). If categorical, data points are colored according to their category.

8. Click the **Calculate** button to generate the scatterplot.

## Method 2: Using a Distance Matrix

1. 1. From the toolbar menu, select **Anything > Advanced Analysis > Dimension Reduction > Dimension Reduction Scatterplot. **

2. Select a distance matrix input:

- Choose an input from the
**Distance matrix**drop-down box which was created in your document, or - Select the paste or type distance matrix to manually input the distance matrix.

From the Select a distance matrix you've created in your document If you've already create a distance matrix in your document using

3. OPTIONAL: Enter a value for **Perplexity** which is a parameter used by the *t-SNE* algorithm and related to the number of nearest neighbors considered when placing each data point. The typical useful range is from 5 to 50 and the default value is 10.

4. Click the **Calculate** button to generate the scatterplot matrix.

## See Also

How to Do Principal Component Analysis in Displayr

How to Create a Principal Component Analysis Biplot

How to Create a Component Plot from a Principal Component Analysis

How to Create a Goodness of Fit Plot from a Dimension Reduction Output

How to Create a Scree Plot from a Principal Component Analysis

How to Save Components/Dimensions from a Dimension Reduction Output

How to do Multidimensional Scaling from Variables

How to do Multidimensional Scaling from a Distance Matrix

How to Create a Distance Matrix

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