iCellR (version 1.6.1)

volcano.ma.plot: Create MA and Volcano plots.

Description

This function takes the result of differential expression (DE) analysis and provides MA and volcano plots.

Usage

volcano.ma.plot(
  x = NULL,
  sig.value = "padj",
  sig.line = 0.1,
  plot.type = "volcano",
  x.limit = 2,
  y.limit = 2,
  limit.force = FALSE,
  scale.ax = TRUE,
  dot.size = 1.75,
  dot.transparency = 0.5,
  dot.col = c("#E64B35", "#3182bd", "#636363"),
  interactive = TRUE,
  out.name = "plot"
)

Arguments

x

A data frame containing differential expression (DE) analysis results.

sig.value

Choose from "pval" or "padj", default = "padj".

sig.line

A number to draw the line for the significant genes based on sig.value type, default = 0.1.

plot.type

Choose from "ma" or "volcano", default = "volcano".

x.limit

A number to set a limit for the x axis.

y.limit

A number to set a limit for the y axis.

limit.force

If set to TRUE the x.limit and y.limit will be forced, default = FALSE.

scale.ax

If set to TRUE the y axis will be scaled to include all the points, default = TRUE.

dot.size

A number for the size of the points in the plot, default = 1.75.

dot.transparency

Color transparency for points in "scatterplot" and "boxplot", default = 0.5.

dot.col

A set of three colors for the points in the volcano plot, default = c("#E64B35","#3182bd","#636363").

interactive

If set to TRUE an interactive HTML file will be created, default = TRUE.

out.name

If "interactive" is set to TRUE, the output name for HTML, default = "plot".

Value

Plots

Examples

# NOT RUN {
diff.res <- run.diff.exp(demo.obj, de.by = "clusters", cond.1 = c(1), cond.2 = c(2))

volcano.ma.plot(diff.res,
              sig.value = "pval",
              sig.line = 0.05,
              plot.type = "volcano",
              interactive = FALSE)

volcano.ma.plot(diff.res,
             sig.value = "pval",
             sig.line = 0.05,
             plot.type = "ma",
             interactive = FALSE)

# }