Create Manhattan Plot — plot_manhattan • libml

Creates a Manhattan plot of the differences or log-ratios of the training set for each feature.

Usage

plot_manhattan(
  data,
  x.lab = "Feature",
  type = c("t.test", "log2fc", "ks.test"),
  as_pvalue = FALSE
)

Arguments

data: A training data tr_data object.
x.lab: character(1). Set the x-axis label.
type: character(1). The type measure used to evaluate expression change. One of: "log2fc", "t.test", or "ks.test". Pattern is matched.
as_pvalue: logical(1). Should p-values be plotted in linear space or log10-space?

Author

Stu Field

Examples

tr <- create_train(simdata,
                   class_response %in% c("control", "disease"),
                   group_var = class_response,
                   classes = c("control", "disease"))

# Various options for plotting
plot_manhattan(tr, type = "t")

plot_manhattan(tr, type = "log2")

plot_manhattan(tr, type = "ks")

plot_manhattan(tr, type = "t", as_pvalue = TRUE)