Entering edit mode
5.9 years ago
Leite
★
1.3k
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
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).
Dear Alex Reynolds, Thanks for the tip, next time I'll put it as indicated.
Best, Leite
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 missingGroups
* Layer 1 is missingGroups
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.
Thanks in advance.
Best regards, Pradeep
I think it is showing the error because you have mentioned "Groups" instead of "Group" for x axis.