Help with Volcano plot
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4 months 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.

enter image description here

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)
Volcano r plot ggplot • 968 views
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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.

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Yes, probably used the Seurat default

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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.

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Please change the threshold to 0.0. This will mean, however, that FindMarkers() takes longer to complete.

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enter image description hereTried. However, the plot does not look well volcanic.

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That looks like a normal volcano plot. What problem do you see with it?

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I thought it's too much merged at the center and in a proper volcano shape. This is my first experience with these plots.

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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.

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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].

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