volcano.ma.plot {iCellR} | R Documentation |
This function takes the result of differential expression (DE) analysis and provides MA and volcano plots.
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" )
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". |
Plots
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)