DEenrichRPlot | R Documentation |
DE and EnrichR pathway visualization barplot
DEenrichRPlot(
object,
ident.1 = NULL,
ident.2 = NULL,
balanced = TRUE,
logfc.threshold = 0.25,
assay = NULL,
max.genes,
test.use = "wilcox",
p.val.cutoff = 0.05,
cols = NULL,
enrich.database = NULL,
num.pathway = 10,
return.gene.list = FALSE,
...
)
object |
Name of object class Seurat. |
ident.1 |
Cell class identity 1. |
ident.2 |
Cell class identity 2. |
balanced |
Option to display pathway enrichments for both negative and positive DE genes.If false, only positive DE gene will be displayed. |
logfc.threshold |
Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25. Increasing logfc.threshold speeds up the function, but can miss weaker signals. |
assay |
Assay to use in differential expression testing |
max.genes |
Maximum number of genes to use as input to enrichR. |
test.use |
Denotes which test to use. Available options are:
|
p.val.cutoff |
Cutoff to select DE genes. |
cols |
A list of colors to use for barplots. |
enrich.database |
Database to use from enrichR. |
num.pathway |
Number of pathways to display in barplot. |
return.gene.list |
Return list of DE genes |
... |
Arguments passed to other methods and to specific DE methods |
Returns one (only enriched) or two (both enriched and depleted) barplots with the top enriched/depleted GO terms from EnrichR.
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