Dividing the groups on the same axis using ggplot2
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Entering edit mode
3.4 years ago
Leite ★ 1.2k

Initially I asked a question of how to make a dotplot from a list of pathways. I was able to generate the graph, but now I can not make the groups side by side using the pathways of reference.

I do not know if that's how I tabulated my results, or if it's a problem with my code, could anyone help me?

My data

My code

data <- read.csv("S3.csv", sep =";", header = TRUE, stringsAsFactors = FALSE)
library("ggplot2")
S3<- ggplot(data, aes(x="Groups", y=Pathways, size=DEGs, color=FDR)) + geom_point(alpha = 0.8) + facet_grid(Group ~ .) + theme_classic()
S3
S3 = S3+scale_color_gradient(low = "red2",  high = "mediumblue", space = "Lab", limit = c(0.000000000000000000000000000000000000000000000004, 0.03))
S3+scale_size(range = c(2, 8))
S3


My result

How do I want the dotplot look like (Edited image)

Best regards, Leite

ggplot2 r dotplot graph • 2.1k views
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Entering edit mode

When pasting data, please consider using text instead of a screenshot. Graphics cannot be copied and pasted into a form where your plot script can be tested.

Using text helps make questions that are easily reproducible and thus easier to answer (and so easier to help you).

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Entering edit mode

Dear Alex Reynolds, Thanks for the tip, next time I'll put it as indicated.

Best, Leite

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Entering edit mode

Dear Leite,

I tried your code to generate dot plot, however, I was getting the following error:

Error: At least one layer must contain all faceting variables: Groups. * Plot is missing Groups * Layer 1 is missing Groups

input format in .csv: Pathway DEGs Padj Groups BILE_ACID_METABOLISM 42 0.0009 Upreg COAGULATION 28 0.0163 Upreg

code: data <- read.csv("pathway_dotplot.csv", sep =";", header = TRUE, stringsAsFactors = FALSE) library("ggplot2") dp<- ggplot(data, aes(x="Groups", y=Pathway, size=DEGs, color=Padj)) + geom_point(alpha = 0.8) + facet_wrap(Group ~ .) + theme_classic()

Not sure what I was doing different from yours.

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Entering edit mode

I think it is showing the error because you have mentioned "Groups" instead of "Group" for x axis.

ggplot(data, aes(x=Group, y=Pathway, size=DEGs, color=Padj)) +
geom_point(alpha = 0.8) +
facet_wrap(Group ~ .) +
theme_classic()

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Entering edit mode
3.4 years ago
Prakash ★ 2.2k

You need to just use facet_wrap(Group ~ .) instead of facet_grid

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Entering edit mode

Dear Prakash

This is exactly what I was looking for. Thank you so much!

Best, Leite

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