Make a static density plot with ggplot2

Usage

static_densityplot(
  plotmatrices,
  experiment,
  colorby = NULL,
  palette = NULL,
  expressiontype = "expression",
  base_size = 16,
  palette_name = COLORBLIND_PALETTE_NAME,
  annotate_samples = FALSE,
  should_transform = NULL
)

Arguments

plotmatrices: Expression/ other data matrix, or named list thereof
experiment: Annotation for the columns of plotmatrix
colorby: Column name in experiment specifying how lines should be colored
palette: Palette of colors, one for each unique value derived from colorby.
expressiontype: Expression type for use in y axis label
base_size: Passed to ggplot's theme()
palette_name: Valid R color palette name
annotate_samples: Add a suffix to sample labels reflecting their group?
should_transform: A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.

Value

output A ggplot output

Examples

mat <- matrix(rnorm(24, mean = 10), nrow = 6, ncol = 4,
  dimnames = list(paste0("gene", 1:6), paste0("s", 1:4)))
experiment <- data.frame(
  condition = rep(c("treated", "control"), each = 2),
  row.names = colnames(mat)
)
static_densityplot(mat, experiment, colorby = "condition")