The spatial differential expression algorithm also you to perform differential expression analysis on spatial data, utilizing special algorithms that take into account the spatial component of the gene expression data.
TABLE OF CONTENTS
- 1 Algorithm settings
- 2. Spatial differential expression interactive plot page
- 2.1 Plot parameters
- You can also look at the differential analysis table by clicking on Show data table in the Visualization - Plot parameters tab. The table is interactive and sortable by clicking on column headers.
- 2.2 Highlight features
- 2.3 Marker format and color for numerical variables
- 2.4 Details
- 2.5 Axes style
- 2.6 Export settings
1 Algorithm settings
1.1 Creating a plot
As a first step in running the analysis, a plot must be created by clicking on the create plot icon in your analysis track. This will lead to a section where the analysis of interest can be selected.
In order to ensure efficient organization, a name and description must be assigned to the analysis under the appropriate fields. Subsequently under "Choose algorithm to run your analysis" Spatial analysis must be selected.
1.2 Selecting data
In the field "Choose track element", the input analysis can be selected. In the cell selection tab you can choose the observations to use as input. For more information see the section on Cell/sample selection.
1.3 Selecting parameters
There are two available algorithms. Mark variogram for which you can set the r value at which to report the “trans” value of the mark variogram and number of top highly varying features to subset by. The Moran's I algorithm has no additional parameters to set.
2. Spatial differential expression interactive plot page
Once you run the spatial differential expression algorithm you can explore the results interactively in the spatial differential expression interactive plot page.
2.1 Plot parameters
You can also look at the differential analysis table by clicking on Show data table in the Visualization - Plot parameters tab. The table is interactive and sortable by clicking on column headers.
2.2 Highlight features
In the Highlight features tab you can set the parameters to decide which features to highlight on the volcano plot. This can be done either by metric or by providing a custom list of features.2.2.1 Highlight features - gene metrics
2.2.2 Highlight features - custom gene list
2.3 Marker format and color for numerical variables
In the Marker format and color tab you can change the appearance of the markers on the volcano plot.Marker symbol: change marker symbol.
Marker size: adjust marker size.
Marker opacity: adjust marker opacity.
2.4 Details
The Details tab contains additonal options for customizing your plot.2.4.1 Grid style
Grid width: adjusts grid width.
Grid color: changes grid color.
Border width: changes width of plot border.
2.4.2 Title style
2.4.3 Plot margins
2.5 Axes style
2.6 Export settings
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