SEplot | R Documentation |
Visualization of SE genes analysis
SEplot( object, diffgenes = diffgenes, topgenes = 100, method = "Integrated", outputFolder = NULL, savePlot = TRUE, Species = NULL, category = "C2", Geneformat = "gene_symbol", ... )
object |
a giotto object |
diffgenes |
A list out of SE-genes calculation. |
topgenes |
Integer; set how many top SE-genes to take, default as 100. |
method |
A character to select the SE method for downstream analysis, one of "Binspect","silhouetteRank","SPARK", "SpatialDE" & "Integrated". |
outputFolder |
Output folder to save results. |
savePlot |
Boolean, whether to save plot. |
Species |
Species name, more details in |
category |
MSigDB collection abbreviation, such as H or C1. |
Geneformat |
Format of gene name in count matrix, one of "ensembl_gene", "gene_symbol". |
... |
other arguments |
ggplot object
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