How do I link my data in glue genes?#
This guide shows you how to link together multiple datasets in glue genes so that they may be plotted simultaneously on the same viewers and so that subsets defined on one dataset will propagate to the other. In general, if you have multiple datasets in glue genes you will want to link them together to unlock the exploratory power of glue.
Open the Link Editor#
Use either the Link Data icon in the glue toolbar or the Link Data menu option in the Data Manager menu to open up the Link Editor – the interface in which you can define links between datasets.
If your datasets have the same attributes…#
If more than one of your datasets describe the same attributes or quantities, then you can tell glue that these mean the same thing. For instance, if you have two different datasets with experiments that both contain the weight of mice, you can set up an Identity Link between these two components, and now if you select a range of weights on, for example, a histogram, that will define a subset on both datasets.
You might also have an image and a table of information about locations in the image. By defining the links between these pixel locations, you can both over-plot the information on the image and have selections on the image define subsets on the table.
In the following example, one dataset is an image and the other dataset is a table of information obtained at a particular location (encoded in pixel coordinates). This is an Identity Link, the simplest kind of link between attributes.
Do the following steps:
1. Identify the names of the columns/components/attributes that contain the pixel locations. If you don’t know this already, create a Table Viewer to look at your data inside glue.
2. Select the two datasets you wish to join either by clicking on them in the central widget shows all the data sets as circles, or by selecting them in the drop downs at the left side of the Link Editor (choosing Dataset 1 and Dataset 2). Note that two datasets will be selected by default, so if you only have two datasets they will already be selected.
3. Choose the components to link on. In this case, we choose Pixel Axis 1 [y] and spatial_0 which encode the y pixel locations in the table data. When the correct components are selected, press the Glue attributes button.
The details of the link will now show on the right-hand panel, and a solid line will show the link between the two datasets in the main display showing links between all datasets.
4. If there are other attributes to join, you can do so now. In this case, we we would also need to join the Pixel Axis 2 [x] and spatial_1 attributes so that the table of information can be shown on top of the image.
If your datasets describe the same items…#
If more than one of your datasets describe the same items, such as the same genes or the same experimental IDs, then you can use the Link Editor to join these datasets on ID. This kind of join means that any selection of points in one dataset will select points with the same IDs in the other dataset.
In the following example, the two datasets both contain information about genes identified by their Mouse ENSEMBL Gene IDs. These are stored in the data files as columns with different names.
Do the following steps:
1. Identify the names of the columns/components/attributes that contain the two IDs. If you don’t know this already, create a Table Viewer to look at your data inside glue.
2. Select the two datasets you wish to join either by clicking on them in the central widget shows all the data sets as circles, or by selecting them in the drop downs at the left side of the Link Editor (choosing Dataset 1 and Dataset 2).
3. Choose Create advanced link from the central part of the Link Editor, and then Join and Join on ID.
4. The right-hand panel (Link details) will now populate with all the attributes for each dataset selected. Choose the two columns that encode the ID that is common between the two datasets.
5. The datasets will now be shown as connected with a dotted line. Click OK to exit the Link Editor.
More information#
See the section on How Data Linking Works in the glue documentation and the linking framework in the glue developer guide for more information about how glue handles links.
What next?#
Now that you have linked your data you probably want to visualize it.