PlotEnrich: PlotEnrich
In brainImageR: A Framework for visualizing gene set enrichment throughout neurodevelopment
Description
Usage
Arguments
Value
Examples
Description
A quick plot to assess the enrichments returned from testEnrich.
Gene overlap calculated by random chance is plotted on the
x-axis and the gene overlap from the query set on the y-axis. Each
dot represents an individual microdissected tissue. Note that
the signficance estimate is only dependent on the randomly generated
overlaps if the p-values were calculated with the bootstrap procedure.
Usage
1
PlotEnrich(boot)
Arguments
boot
Comp object returned from the testEnrich function
Value
Spatial enrichment plot
Examples
1
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10
#brainImageR:::loadworkspace()
##First put together a gene list, or load in the default vth dataset
data(vth)
##Calculate the spatial enrichment
#composite <- SpatialEnrichment(vth, 20, "developing")
#tissueExp1 <- composite@tissueExp1
#random.matrix <- composite@random.matrix
##Calculate the significance estimates
#boot <- testEnrich(composite)
#PlotEnrich(boot)
brainImageR documentation built on May 6, 2019, 3:54 a.m.
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Description Usage Arguments Value Examples
Description
A quick plot to assess the enrichments returned from testEnrich. Gene overlap calculated by random chance is plotted on the x-axis and the gene overlap from the query set on the y-axis. Each dot represents an individual microdissected tissue. Note that the signficance estimate is only dependent on the randomly generated overlaps if the p-values were calculated with the bootstrap procedure.
Usage
1 | PlotEnrich(boot)
|
Arguments
boot |
Comp object returned from the testEnrich function |
Value
Spatial enrichment plot
Examples
1 2 3 4 5 6 7 8 9 10 | #brainImageR:::loadworkspace()
##First put together a gene list, or load in the default vth dataset
data(vth)
##Calculate the spatial enrichment
#composite <- SpatialEnrichment(vth, 20, "developing")
#tissueExp1 <- composite@tissueExp1
#random.matrix <- composite@random.matrix
##Calculate the significance estimates
#boot <- testEnrich(composite)
#PlotEnrich(boot)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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