Entering edit mode
17 months ago
luzglongoria
▴
50
Hi there,
I'm trying to do a plot like this one:
But I am not able with my command:
ggplot(Heatmap_Go, aes(x = Molecular_function,y=-log10(padj), fill=Cond)) +
theme_classic() +
geom_bar(stat = "identity", position = "dodge",color="black") +
geom_vline(xintercept = 0,colour = "grey90") +
facet_grid(~ Group, switch = "x", scales = "free_x", space = "free_x") +
coord_flip() +
scale_fill_manual(values=c("#ffffff", "#000000")) +
xlab("Molecular function")
With this command I get this:
My data set look like this:
Molecular_function padj Moment Group Cond
nucleic acid binding 0.000389804 d Down regulated Signi
RNA binding 0.003802644 d Down regulated Signi
iron ion binding 0.000460617 d Up regulated Signi
heme binding 0.000953612 d Up regulated Signi
tetrapyrrole binding 0.001045832 d Up regulated Signi
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 0.006341203 d Up regulated Signi
ATP-dependent microtubule motor activity, minus-end-directed 0.007685289 d Up regulated Signi
monooxygenase activity 0.030799501 d Up regulated Signi
transporter activity 0.041251611 d Up regulated Signi
phosphoenolpyruvate carboxykinase activity 0.049891016 d Up regulated Signi
phosphoenolpyruvate carboxykinase (GTP) activity 0.049891016 d Up regulated Signi
iron ion binding 0.58 d Down regulated No_Signi
heme binding 0.41 d Down regulated No_Signi
tetrapyrrole binding 0.21 d Down regulated No_Signi
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 0.87 d Down regulated No_Signi
ATP-dependent microtubule motor activity, minus-end-directed 0.25 d Down regulated No_Signi
monooxygenase activity 0.58 d Down regulated No_Signi
transporter activity 0.26 d Down regulated No_Signi
phosphoenolpyruvate carboxykinase activity 0.14 d Down regulated No_Signi
phosphoenolpyruvate carboxykinase (GTP) activity 0.89 d Down regulated No_Signi
nucleic acid binding 0.398039992 d Up regulated No_Signi
RNA binding 0.802643739 d Up regulated No_Signi
I don't know how to flip the "Down regulated" axis. I just want values starting from the same point : from zero to right and from zero to left.
Any help is more than welcome.
Thank you in advance.
Can you transform your data so your downregulated terms have negative -log10(padj) values?
Maybe not the best way, but an easy one is to use negative values for padj for the down regulated group and afterwards remove the negative values manually or annotate the x axis accordingly. Hope it helps.
Thank you so much. It perfectly worked !