VolcanoDEGRE: Create a volcano plot to visualize the proportion of...

In DEGRE: Inferring Differentially Expressed Genes using Generalized Linear Mixed Models

Create a volcano plot to visualize the proportion of downregulated and upregulated genes by applying a log2FC cutoff.

Description

Create a volcano plot to visualize the proportion of downregulated and upregulated genes by applying a log2FC cutoff.

Usage

VolcanoDEGRE(
  results,
  log2FC_cutoff = 1,
  padj = 0.05,
  font.x = 10,
  font.y = 10,
  font.tickslab = 10,
  downregulated_color = "coral2",
  upregulated_color = "cornflowerblue",
  xlab = "log2Foldchange",
  ylab = "-log10(P-value)",
  legend_position = "right",
  legend.title = "Regulation"
)

Arguments

results	a data.frame object. It receives the output of the DEGRE function, filtered or not, as input.
log2FC_cutoff	it stores the cutoff of the log2FoldChange. The default is 1.
padj	it stores the cutoff of the P-adjusted value (Q-value). The default is 0.05.
font.x	the font size of the x axis. The default is 10.
font.y	the font size of the y axis. The default is 10.
font.tickslab	the font size of the ticks lab. The default is 10.
downregulated_color	the colors of the downregulated genes. The default is "coral2".
upregulated_color	the colors of the upregulated genes. The default is "cornflowerblue".
xlab	the x lab text. The default is "log2Foldchange".
ylab	the y lab text. The default is "-log10(P-value)".
legend_position	you need to specify here the position of the legend. The default is "right".
legend.title	the title of the legend. The default is "Regulation".

Value

No return value, called for side effects

Examples

dir <- system.file("extdata", package = "DEGRE")
results_DEGRE_example <- read.csv(file.path(dir,"results_DEGRE_example.csv"))
# Running the VolcanoDEGRE function
VolcanoDEGRE(results = results_DEGRE_example,
          log2FC_cutoff = 1,
          padj = 0.05,
          font.x = 10,
          font.y = 10,
          font.tickslab = 10,
          downregulated_color = "coral2",
          upregulated_color = "cornflowerblue",
          xlab = "log2Foldchange",
          ylab = "-log10(P-value)",
          legend_position = "right",
          legend.title = "Regulation")

DEGRE documentation built on Nov. 2, 2022, 5:07 p.m.