Scatter plot view of an experiment
At the bottom of the experiment table, you can switch between different views of the experiment (see figure 19.14).
Figure 19.14: An experiment can be viewed in several ways.
One of the views is the Scatter Plot (
). The scatter plot can be adjusted to show e.g. the group means for two groups (see more about how to adjust this below).
An example of a scatter plot is shown in figure 19.15.
Figure 19.15: A scatter plot of group means for two groups (transformed expression values).
In the Side Panel to the left, there are a number of options to adjust this view. Under Graph preferences, you can adjust the general properties of the scatter plot:
- Lock axes. This will always show the axes even though the plot is zoomed to a detailed level.
- Frame. Shows a frame around the graph.
- Show legends. Shows the data legends.
- Tick type. Determine whether tick lines should be shown outside or inside the frame.
- Outside
- Inside
- Tick lines at. Choosing Major ticks will show a grid behind the graph.
- None
- Major ticks
- Horizontal axis range. Sets the range of the horizontal axis (x axis). Enter a value in Min and Max, and press Enter. This will update the view. If you wait a few seconds without pressing Enter, the view will also be updated.
- Vertical axis range. Sets the range of the vertical axis (y axis). Enter a value in Min and Max, and press Enter. This will update the view. If you wait a few seconds without pressing Enter, the view will also be updated.
- Draw x = y axis. This will draw a diagonal line across the plot. This line is shown per default.
- Line width
- Thin
- Medium
- Wide
- Line type
- None
- Line
- Long dash
- Short dash
- Line color. Allows you to choose between many different colors. Click the color box to select a color.
Below the general preferences, you find the Dot properties preferences, where you can adjust coloring and appearance of the dots:
- Dot type
- None
- Cross
- Plus
- Square
- Diamond
- Circle
- Triangle
- Reverse triangle
- Dot
- Dot color. Allows you to choose between many different colors. Click the color box to select a color.
Finally, the group at the bottom - Columns to compare - is where you choose the values to be plotted. Per default for a two-group experiment, the group means are used.
Note that if you wish to use the same settings next time you open a scatter plot, you need to save the settings of the Side Panel.