comparegsea_scatter {SCdeconR} | R Documentation |
Generate a scatter plot comparing two gene set enrichment analysis results
Description
Generate a scatter plot of normalized enrichment scores comparing two results for gene set enrichment analysis, e.g. w/wo adjusting for cell proportion differences.
Usage
comparegsea_scatter(
gseares_path1,
gseares_path2,
result_names = NULL,
nes_cutoff = 2,
pval_cutoff = 0.1,
pvalflag = TRUE,
interactive = FALSE
)
Arguments
gseares_path1 |
path to GSEA output. |
gseares_path2 |
path to a second GSEA output. |
result_names |
a vector of length 2 indicating the names of the two GSEA results. If NULL, names will be set to c("results1", "results2") |
nes_cutoff |
normalized enrichment score cutoff to identify enriched gene-sets. |
pval_cutoff |
p value cutoff to identify enriched gene-sets. |
pvalflag |
a logical value indicating whether to use adjusted p value in selecting enriched gene-sets. Default to TRUE. |
interactive |
a logical value indicating whether to generate an interactive plot. Default to FALSE. |
Details
this function does not support output from GSEA R implementation
Value
a ggplot
object or plotly
object if interactive is set to TRUE