The XY Plot can be used to display the effect of two categorical variables, like time and treatment or dose and treatment, on a response variableplot / bar chart displays the intensity of one probe(set)/gene across two categorical variables. Only one probe(set)/gene may be visualized at a time.

Invoking from a gene list

We will invoke an XY Plot plot from a gene list child spreadsheet with genes on rows. The parent spreadsheet should include the categorical variables you want to chart. 

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An XY Plot plot will be displayed in a new tab (Figure 2). 

• Select () from the plot command bar
• Set X-Axis to 3. Time using the drop-down menu
• Set Separate by to 2. Treatment using the drop-down menu
• Select OK

To help visualize the connection between time points, we can add connecting lines.

• Select ()   from the plot command bar
• Set Plot Style to lines using the drop-down menu
• Select OK

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While most of the plot controls are shared with Dot Plotwith the dot plot, XY Plot plot does have a few unique options. 

• Select Fly Through () to automatically cycle through each row (gene) in the source spreadsheet
• Select () to stop the cycling

Fly Through This feature is useful when performing visual analysis of patterns in gene expression changes in a list of genes. 

The drop-down menu adjacent to the previous/next () controls lets you switch source spreadsheets. 

Lines, but not points, can be selected when using Selection Mode (). 

Invoking from the parent spreadsheet

It is also possible to invoke an XY plot from the parent spreadsheet using the main toolbar.

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To switch this plot from to one of the gene lists we have created, we can use the drop-down menu next to the previous/next controls. 

Bar Chart Plots

The displayed by a XY Plot plot can instead be displayed as a bar chart with overlayed bars, vertically stacked bars, or horizontally stacked bars. A bar chart can be directly invoked or an XY Plot plot can be converted into a bar chart (and vice versa). 

• Invoke the plot from a gene list using the Bar Chart (Orig. Data) option in the pop-up menu (Figure 1)
• Invoke the plot from the main toolbar by selecting one of the bar chart options in the Line Style drop-down menu (Figure 4)
• Invoke the plot as an XY Plotplot, select (), then select one of the bar chart options from the Plot Style drop-down menu in the Plot Rendering Properties dialog (Figure 6)
  
  

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