Is it possible to modify the gene names from the x-axis in Seurat::Dotplot?

Question

[ev97]

I have generated some dotplots for some genes in my scRNAseq data.

As the Seurat object was already annotated with Ensembl IDs (and not gene names), I am struggling a bit trying to replace those IDs to gene names in my plots.

In this context, I am trying to generate a DotPlot for two genes at the same time and although I have tried to specify the gene name, I only managed to put it as a title and not replace it at the bottom (in the x-axis).

Seurat::DotPlot(seuObject,
                    features = list("Gene1" = "ENSXXXXXXXXXX",  "Gene2" = "ENSXXXXXXXXXXX"),  group.by  = "Conditions") + 
        labs(title = "Gene1 & Gene2") + xlab("")

Does anybody know how I could remove the Ensembl IDs (ENSGXXXXX) from the bottom and instead writing the gene names (that I have at the top) in this type of plot?

Thanks very much in advance

Answer 1

[bk11]

Here is how you can change the genes names in DotPlot-

rm(list=ls())
# Load necessary libraries
library(Seurat)
library(SeuratData)
library(ggplot2)
library(patchwork)

data=UpdateSeuratObject(pbmc3k.final)

# Assume 'seurat_object' is your Seurat object and 'genes' is the list of genes you are plotting
genes <- c("MS4A1", "TAL1", "IPP")

# Create a DotPlot
p1 <- DotPlot(data, features = genes) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
dot_plot <- DotPlot(data, features = genes)

# Custom gene labels - ensure this vector is in the same order as 'genes'
custom_labels <- c("Custom_Label1", "Custom_Label2", "Custom_Label3")

# Replace the gene names in the plot
dot_plot$data$features.plot <- factor(dot_plot$data$features.plot, 
                                      levels = genes, 
                                      labels = custom_labels)

# Display the modified DotPlot
p2 <- dot_plot + theme(axis.text.x = element_text(angle = 45, hjust = 1))

p1|p2

[ev97]

Just what I wanted. It works perfectly. Thanks a lot!

[ev97]

Just in case someone gets to this post with the same question but using SCpubr::do_DotPlot, you can use the same accepted answer adding an extra line of code:

dot_plot$data$features.plot <- factor(dot_plot$data$features.plot, 
                                      levels = genes, 
                                      labels = custom_labels)

 #addition
p <- p + scale_x_discrete(labels = genes)