volcanoPlot()

Adrià Mitjavila Ventura

Source: vignettes/03-volcanoPlot.Rmd

Load plotmics 

# load plotmics
library(plotmics)

Run volcanoPlot()

volcanoPlot() draws an ggplot2-based volcanoPlot with the Log2(fold change) at the X axis and the -Log10(adjusted p-value) in the Y axis.

Required

As input, barDEGs takes a data frame with the columns Geneid, log2FoldChange, padj and DEG. The DEG column must have the values Upregulated, Downregulated and NS.

# read the dataframes into a list
deg_list <- list.files("../testdata", "diff_exp", full.names = T, recursive = T) %>%
  purrr::set_names(paste("cond", 1:3, sep = "")) %>%
  purrr::map(~read.delim(.x))

deg_list[[1]] %>% head()
##   Geneid               ENSEMBL log2FoldChange         padj           DEG
## 1 Gsdmc2 ENSMUSG00000056293.12           2.69 9.334654e-29   Upregulated
## 2 Gsdmc4 ENSMUSG00000055748.12           2.66 1.060432e-28   Upregulated
## 3   Car4 ENSMUSG00000000805.18           2.11 1.883150e-25   Upregulated
## 4 Duoxa2  ENSMUSG00000027225.7           2.97 2.097922e-22   Upregulated
## 5  Neat1  ENSMUSG00000092274.3          -2.25 2.097922e-22 Downregulated
## 6 Gsdmc3 ENSMUSG00000055827.13           2.51 9.601422e-20   Upregulated

Minimum run 

volcanoPlot(df = deg_list[[1]])

Change thresholds 

volcanoPlot(df = deg_list[[1]], log2FC = 4, pval = 0.001)

Customize plot

Change axis limits 

volcanoPlot(df = deg_list[[1]], xlim = c(-5,5), ylim = c(0,10))

Draw grid lines 

volcanoPlot(df = deg_list[[1]], gridLines = T)

Specify titles 

volcanoPlot(df = deg_list[[1]], main = "This is a title", sub = "This is a subtitle", 
            xlab = "This is the X-axis label", ylab = "This is the Y-axis label")

volcanoPlot(df = deg_list[[1]], main = "This is a title", sub = "This is a subtitle", 
            xlab = "This is the X-axis label", ylab = "This is the Y-axis label", 
            mainSize = 19, subSize = 15, axisLabelSize = 14, 
            axisTextSize = 15)

Change DEG numbers

Change size of DEG number labels

volcanoPlot(df = deg_list[[1]], labelSize = 12)

Change color of DEG number labels

volcanoPlot(df = deg_list[[1]], labelColor = c("gold4", "blue"))

volcanoPlot(df = deg_list[[1]], labelColor = c("black"))

Change position of DEG number labels

volcanoPlot(df = deg_list[[1]], labelPos = 30)

Change point colors 

volcanoPlot(df = deg_list[[1]], pointColor = c("cornflowerblue", "gray", "gold3"))

Show genes names

5 most significant genes

volcanoPlot(df = deg_list[[1]], degsLabel = T)
## Loading required package: ggrepel

Change number of genes to show

volcanoPlot(df = deg_list[[1]], degsLabel = T, degsLabelNum = 20)
## Warning: ggrepel: 17 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

Show wanted genes

genes_to_show <- c("Lef1", "Mtor", "Ctnna1")

volcanoPlot(df = deg_list[[1]], degsLabel = genes_to_show, degsLabelSize = 5)

Change size of gene labels

volcanoPlot(df = deg_list[[1]], degsLabel = T, degsLabelSize = 10)

Further costumization

Since barDEGs() outputs a ggplot2-based scatter plot, it can be further customized with scales or theme, etc.