volcano.ma.plot | 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 = F, scale.ax = T, 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", defult = "padj". |
sig.line |
A number to draw the line for the significant genes based on sig.value type, defult 0.1. |
plot.type |
Choose from "ma" or "volcano", defult = "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, defult = FALSE. |
scale.ax |
If set to TRUE the y axis will be scaled to include all the points, defult = TRUE. |
dot.size |
A number for the size of the points in the plot, defult = 1.75. |
dot.transparency |
Color transparency for points in "scatterplot" and "boxplot", defult = 0.5. |
dot.col |
A set of three colors for the points in the volcano plot, defult = c("#E64B35","#3182bd","#636363"). |
interactive |
If set to TRUE an intractive HTML file will be created, defult = TRUE. |
out.name |
If "interactive" is set to TRUE, the out put name for HTML, defult = "plot". |
Plots
## Not run: volcano.ma.plot(diff.res, sig.value = "pval", sig.line = 0.05, plot.type = "volcano", interactive = T, out.name = "Volcano.plot-Control2_vs_Treated3") volcano.ma.plot(diff.res, sig.value = "pval", sig.line = 0.05, plot.type = "ma", interactive = T, out.name = "MA.plot-Control2_vs_Treated3") ## End(Not run)
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