the data: dput(gsea)
structure(list(ID = c("ab1", "ab2", "ab3", "ab4", "ab5", "ab6",
"ab7", "ab8", "ab9", "ab10", "ab11", "ab12", "ab13", "ab14",
"ab15", "ab16", "ab17", "ab18", "ab19", "ab20"), Count = c(183L,
37L, 15L, 30L, 38L, 98L, 49L, 58L, 43L, 49L, 98L, 10L, 15L, 83L,
14L, 5L, 129L, 69L, 32L, 19L), NES = c(3.115511918, 2.65379757,
2.385595991, 2.310872715, 2.166809058, 2.157225827, 2.112706611,
-1.982794655, -1.96510639, -1.890716501, -1.845158581, 1.843252451,
-1.833650877, -1.832752633, 1.830915101, 1.827824231, -1.804884734,
-1.79943276, -1.786694788, -1.779892361), pvalue = c(1.4e-43,
6.72e-12, 3.55e-07, 6.6e-08, 8.33e-07, 8.16e-14, 1.31e-08, 1.01e-06,
7.33e-06, 5.55e-05, 8.32e-06, 0.002090754, 0.0008865, 1.06e-06,
0.003576374, 0.005822333, 7.09e-08, 3.15e-05, 0.000196647, 0.001113372
), REG = c("up", "up", "up", "up", "up", "up", "up", "down",
"down", "down", "down", "up", "down", "down", "up", "up", "down",
"down", "down", "down"), ABS = c(3.115511918, 2.65379757, 2.385595991,
2.310872715, 2.166809058, 2.157225827, 2.112706611, 1.982794655,
1.96510639, 1.890716501, 1.845158581, 1.843252451, 1.833650877,
1.832752633, 1.830915101, 1.827824231, 1.804884734, 1.79943276,
1.786694788, 1.779892361)), class = "data.frame", row.names = c(NA,
-20L))
I tried to plot using the following code:
ggplot(gsea, aes(reorder(ID, NES), NES)) +
geom_col(aes(fill=NES<0)) +
scale_color_manual(name = 'NES', labels = c("Suppressed", "Activated"), values = c(`FALSE` = 'green', `TRUE` = 'red'))+
coord_flip() +
labs(x="Pathway", y="Normalized Enrichment Score",
title="Curated pathways GSEA") +
theme_minimal()
Generated output:
I want to change the label TRUE to Activated and DOWN to Suppressed. and NES > 0 to regulation ? How do I do it?
>Solution :
You can try as:
ggplot(df, aes(reorder(ID, NES), NES)) +
geom_col(aes(fill=REG)) +
scale_color_manual(name = 'REG')+
coord_flip() +
labs(x="Pathway", y="Normalized Enrichment Score",
title="Curated pathways GSEA") +
theme_minimal()