R: Plot clusters from degPattern function output

degPlotCluster {DEGreport}

R Documentation

Plot clusters from degPattern function output

Description

This function helps to format the cluster plots from degPatterns(). It allows to control the layers and it returns a ggplot object that can accept more ggplot functions to allow customization.

Usage

degPlotCluster(table, time, color = NULL, points = TRUE,
  boxes = TRUE, smooth = TRUE, lines = TRUE, facet = TRUE)

Arguments

`table`	`normalized` element from `degPatterns()` output.
`time`	column name to use in the x-axis.
`color`	column name to use to color and divide the samples.
`points`	Add points to the plot.
`boxes`	Add boxplot to the plot.
`smooth`	Add regression line to the plot.
`lines`	Add gene lines to the plot.
`facet`	Split figures based on cluster ID.

Value

ggplot2 object.

Examples

data(humanGender)
library(SummarizedExperiment)
library(ggplot2)
ma <- assays(humanGender)[[1]][1:100,]
des <- colData(humanGender)
des[["other"]] <- sample(c("a", "b"), 85, replace = TRUE)
res <- degPatterns(ma, des, time="group", col = "other", plot = FALSE)
degPlotCluster(res$normalized, "group", "other")
degPlotCluster(res$normalized, "group", "other", lines = FALSE)

[Package DEGreport version 1.18.1 Index]