# Dot Plot

The primary use of the dot plot is visualizing intensity values across samples.

We will invoke a dot plot from a gene list child spreadsheet with genes on rows.

* Right-click on the row header of the gene you want to visualize
* Select **Dot Plot** from the pop-up menu (Figure 1)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-51c76c15a14a9b638d86ce058aed544c74e6385c%2F2017-08-15%2012_04_04-Partek%20Genomics%20Suite%20-%201_Down_Syndrome_vs_Normal%20\(A\).png?alt=media)

Figure 1. Creating a dot plot of gene intensity values

A dot plot will be displayed in a new tab (Figure 2).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d4048e888ecc0ea8d69e149cd0e3e16ddcb0779b%2F2017-08-15%2012_07_25-Partek%20Genomics%20Suite%20-%201_Down_Syndrome_vs_Normal%20\(A\).png?alt=media)

Figure 2. Simple dot plot of a single gene that shows the distribution of intensities across all samples

There are many customizations that can be made to this simple plot.

* Select **Configure Plot (**![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9b42496a94328761e155dabd3ca0939e99d73ec8%2Fimage2017-8-15%2012_10_25.png?alt=media)**)** from the plot command bar to launch the *Configure Plot* dialog (Figure 3).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d5dca2348fb9af5cc38fa4c26695fcaf3ad35511%2F2017-08-15%2012_12_08-Configure%20Plot.png?alt=media)

Figure 3. Configuring the data shown on the plot

The *Configure Plot* dialog lets you change how the data is displayed on the plot. We will make a change to illustrate the possibilities.

* Set *Group by* to **4. Tissue** using the drop-down menu

This allows us to group the samples by any categorical attribute. These attributes are specified in the parent spreadsheet.

* Select **OK** to modify the plot

We could also have changed the grouping of samples using the *Group by* drop-down menu above the plot.

The order of the group columns is alphabetical by default, but can be changed to match the spreadsheet order by selecting **Categoricals in spreadsheet order** in the *Configure Plot* dialog (Figure 3).

* Select **Plot Properties (**![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8686f111655525c6027f24eb07460a3a65b27fe2%2Fimage2017-8-29%2013_10_8.png?alt=media)**)** from the plot command bar to launch the *Plot Properties* dialog (Figure 4)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-3f170d3bc0da927b2dc9823c0c3f15f205b5a010%2F2017-08-15%2012_24_10-Plot%20Rendering%20Properties.png?alt=media)

Figure 4. Changing the appearance of a dot plot using the plot properties dialog

The *Plot Properties* dialog lets you change the appearance of the plot. We will make a few changes to illustrate the possibilities.

* Set *Shape* to **3. Type** using the drop-down menu
* Select the **Box\&Whiskers** tab
* Set *Box Width* to **15** pixels
* Select the **Titles** tab
* Set *X-Axis* under *Configure Axes Titles* to Tissue
* Select **OK** to modify the plot

Alternately, we chould have changed the shapes using the *Shape by* drop-down menu above the plot. The dot plot now shows four columns with thinner box and whisker plots for each and different shapes for different sample types (Figure 5).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-7176e4ce5e4387583d9e3848bad0aaa30ce81766%2F2017-08-15%2012_37_50-Partek%20Genomics%20Suite%20-%201_Down_Syndrome_vs_Normal%20\(A\).png?alt=media)

Figure 5. The Dot Plot can be modified to optimally visualize your data

Like many visualizations in Partek Genomics Suite, the dot plot is interactive.

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-bf3137376af6b29cc74118ff864c624725453ec1%2Fimage2017-8-15%2012_56_54.png?alt=media)) to activate Selection Mode

Legends can now be dragged and dropped to new locations on the plot. Samples can be selected by left-clicking the sample or left-clicking and dragging a box around samples.

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8fc746c75f830696bb32e61ee1a05dad5951d76b%2Fimage2017-8-15%2013_0_3.png?alt=media)) to activate Zoom Mode

Left clicking on a region will zoom in on it. The zoom level can be reset by selecting (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-2c54834fb5f31424745a38e6a1c6033ec796724b%2Fimage2017-8-15%2013_1_24.png?alt=media)).

* After zooming in, select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-121c7c82c9bafa244911d02a62ec407e3f48cdd2%2Fimage2017-8-15%2013_2_48.png?alt=media)) to activate Pan Mode

Left-click and drag to move around the plot.

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-54c28044351d159e805768b6024eb22a2d6a13ff%2Fimage2017-8-15%2013_4_2.png?alt=media)) to move between rows on the source spreadsheet
* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-065b42ae8addbb9e8c589041a8b04994e63cd1aa%2Fimage2017-8-15%2013_6_51.png?alt=media)) to swap the horizontal and vertical axes

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