DEseq2 result file figure between Genus and log2fold change
Hello
Could you please suggest how I can get dotplot figure like attached from deseq2 result file; My deseq2 result file looks like this;
I wanted to show Genus names on Y-axis and log2Foldchange on the X-axis and I am also wanted to show dot colour based on phylum name.
log2FoldChange padj Kingdom Phylum Genus
OTU1 0.214360038 0.369800256 Bacteria Proteobacteria Burkholderiaceae
OTU2 0.104133836 0.611791812 Bacteria Proteobacteria Xanthobacteraceae
OTU3 0.911214638 8.33E-08 Bacteria Proteobacteria Archangiaceae
OTU4 1.162701206 4.80E-08 Bacteria Proteobacteria Geobacteraceae
OTU5 -2.439651618 1.62E-08 Bacteria Actinobacteria Microbacteriaceae
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Bioinfonext
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1 answer
Example data.
df <- structure(list(log2FoldChange = c(0.214360038, 0.104133836, 0.911214638,
1.162701206, -2.439651618), padj = c(0.369800256, 0.611791812,
8.33e-08, 4.8e-08, 1.62e-08), Kingdom = c("Bacteria", "Bacteria",
"Bacteria", "Bacteria", "Bacteria"), Phylum = c("Proteobacteria",
"Proteobacteria", "Proteobacteria", "Proteobacteria", "Actinobacteria"
), Genus = c("Burkholderiaceae", "Xanthobacteraceae", "Archangiaceae",
"Geobacteraceae", "Microbacteriaceae")), class = "data.frame", row.names = c("OTU1",
"OTU2", "OTU3", "OTU4", "OTU5"))
ggplot2 solution.
library("forcats")
library("ggplot2")
df %>%
mutate(Genus=fct_reorder(Genus, log2FoldChange)) %>%
ggplot(aes(x=log2FoldChange, y=Genus)) +
geom_vline(xintercept=0) +
geom_point(aes(color=Phylum), size=5)
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