From Array Suite Wiki
Creating a BoxPlot
One common way to plot expression data, such as RNA-seq FPKM values or microarray intensity, is as a "Variable View" grouped by metadata (such as tissue, disease state, etc.). These data can then be grouped by metadata, and the range of expression can be summarized with a BoxPlot.
Input Data Requirements
Step 1: Create Variable View of expression data
The user can add a "Variable" view by right-clicking on the -Omic data object and clicking "Add View", then selecting "Variable View":
In a Variable View, one plot will show the expression for one variable (e.g. gene), plotted for each sample.
Step 2: Group expression data by metadata
Samples can then be grouped by metadata (e.g. tissue):
to show the range of expression by that category:
Step 3a (optional): Color by additional metadata
The individual data points ("symbols") can also be colored by metadata, such as detailed tissue information, and also add "Jitter" to reduce overlap of data points:
which will allow you see similarities and differences in expression within primary grouping:
Step 4: Add BoxPlot
Now the user can change the "plotting profile" by clicking Change Profile Gallery:
The "Classic" BoxPlot will display a box bounded by the 25% and 75% ranked sample, with a line indicating the median, and the "whiskers" will indicate the range to the minimum and maximum value for that group. All values will be plotted unless explicitly filtered out under "Outlier option".
The "R-Style" BoxPlot will display a box bounded by the 25% and 75% ranked sample, with a line indicating the median, and the "whiskers" will indicate the bounds of 1.5*IQR (Inter-quartile range). Only values outside the whiskers will be plotted.
Revised BoxPlot (RBoxPlot)
The "Revised" BoxPlot (RBoxPlot) will display a box bounded by the 25% and 75% ranked sample, with a line indicating the median, and the "whiskers" will indicate the bounds of 1.5*IQR (Inter-quartile range). Like the Classic BoxPlot, all values will be plotted.
(Optional) Creating a Land-style BoxPlot
ArrayLand expressions are by default plotted as "Revised" BoxPlots, but FPKM values are log2-transformed. To emulate the plots you see in Land:
- Select RBoxPlot under Change Profile Gallery
- Select Flip X/Y Axis under Task | Properties in the View Controller
- Select Change Fill Properties under Task | Properties, change opacity to 50%, and change fill color to red.
- Select Specify Transformation under Task | Data, and select Log2xPlus0_1