Entering edit mode
3.4 years ago
mshubham
•
0
Hi, I am having difficulty in plotting the volcano plot. I used ggplot to plot the graph, but my graph is blank at the center across Log2Fc=0. I am not able to understand why there is no dots at centre whereI do have some genes being expressed in this region. Please do help.
threshold_OE <- As.response$p_val < 0.05
As.response$threshold <- threshold_OE
P24 <- ggplot(As.response) +
geom_point(aes(x=avg_log2FC, y=-log10(p_val), color = threshold)) +
ggtitle("Astrocyte response") +
xlab("log2 fold change") +
ylab("-log10 p-value") +
#scale_y_continuous(limits = c(0,50)) +
theme(legend.position = "none",
plot.title = element_text(size = rel(1.5), hjust = 0.5),
axis.title = element_text(size = rel(1.25)))
P25 <- LabelPoints(plot = P24, points = genes.to.label.As.new, xnudge = 0, ynudge = 0, repel = TRUE)
what code did you use to generate
As.response? It looks like genes with a |log2 fold change| < 0.25 were potentially filtered out of the data.Yes, probably used the Seurat default
Hi, Yes, possibly due to As.response was generated by using FindMarker() with 0.25 as a cutoff. Please let me know if there is a better way to plot the differential expression data generated by Seurat.
Please change the threshold to 0.0. This will mean, however, that
FindMarkers()takes longer to complete.That looks like a normal volcano plot. What problem do you see with it?
I thought it's too much merged at the center and in a proper volcano shape. This is my first experience with these plots.
How can I annotate the pathways associated with the genes labeled above? Since they are very small set of genes, I only want to annotate the pathway, not perform enrichment analysis.
Please use KEGGprofile (I just posted an answer here: https://support.bioconductor.org/p/9138854/), or some other pathway analysis program. Anyway, this is a new question that is very much unrelated to the original [question].