Volcano plot for visualizing differentailly expressed genes.

Usage

volcano_plot(
  data,
  title = "CT-vs-LT12",
  log2fc_cutoff = 1,
  pq_value = "pvalue",
  pq_cutoff = 0.05,
  cutoff_line = "longdash",
  point_shape = "large_circle",
  point_size = 2,
  point_alpha = 0.5,
  color_normal = "#888888",
  color_log2fc = "#008000",
  color_pvalue = "#0088ee",
  color_Log2fc_p = "#ff0000",
  label_size = 3,
  boxed_labels = FALSE,
  draw_connectors = FALSE,
  legend_pos = "right"
)

Arguments

data: Dataframe: differentially expressed genes (DEGs) stats (1st-col: Genes, 2nd-col: log2FoldChange, 3rd-col: Pvalue, 4th-col: FDR).
title: Character: title of plot. Default: CT-vs-LT12.
log2fc_cutoff: Numeric: log2(FoldChange) cutoff log2(2) = 1. Default: 1.0, min: 0.0, max: null.
pq_value: Character: select pvalue or qvalue. Default: "pvalue", options: "pvalue", "padj".
pq_cutoff: Numeric: pvalue or qvalue cutoff. Default: 0.005, min: 0.000, max: 1.000.
cutoff_line: Character: cutoff line type. Default: "longdash", options: "blank", "solid", "dashed", "dotted", "dotdash", "longdash", "twodash".
point_shape: Character: point shape. Default: "large_circle", options: "border_square", "border_circle", "border_triangle", "plus", "times", "border_diamond", "border_triangle_down", "square_times", "plus_times", "diamond_plus", "circle_plus", "di_triangle", "square_plus", "circle_times","square_triangle", "fill_square", "fill_circle", "fill_triangle", "fill_diamond", "large_circle", "small_circle", "fill_border_circle", "fill_border_square", "fill_border_diamond", "fill_border_triangle".
point_size: Numeric: point size. Default: 1.0, min: 0.0, max: null.
point_alpha: Numeric: point color alpha. Default: 0.50, min: 0.00, max: 1.00.
color_normal: Character: normal genes color (color name or hex value). Default: "#888888".
color_log2fc: Character: genes color that log2fc >= log2fc_cutoff. Default: "#008000".
color_pvalue: Character: genes color that pvalue > pq_cutoff. Default: "#0088ee".
color_Log2fc_p: Character: genes color that log2fc >= log2fc_cutoff and pvalue > pq_cutoff. Default: "#ff0000".
label_size: Numeric: DEG labels size. Default: 3.0, min: 0.0, max: null.
boxed_labels: Logical: add box to every DEG label. Default: FALSE.
draw_connectors: Logical: add connector between DEGs and labels. Default: FALSE.
legend_pos: Character: legend position. Default: "right", options: "right", "left", "top", "bottom".

Value

Plot: volcano plot for visualizing differentailly expressed genes.

Author

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(degs_stats)
head(degs_stats)
#>    Gene log2FoldChange      Pvalue         FDR
#> 1  A1I3    -1.13855748 0.000111040 0.000862478
#> 2   A1M     0.59076131 0.070988041 0.192551708
#> 3   A2M     0.09297827 0.819706797 0.913893947
#> 4 A2ML1    -0.26940689 0.745374782 0.874295125
#> 5  ABAT     1.24811621 0.000001440 0.000016800
#> 6 ABCC3    -0.72947545 0.005171574 0.024228298

# 3. Default parameters
volcano_plot(degs_stats)


# 4. Set color_Log2fc_p = "#ff8800"
volcano_plot(degs_stats, color_Log2fc_p = "#ff8800")


# 5. Set boxed_labels = TRUE
volcano_plot(degs_stats, boxed_labels = TRUE)