plotPDX {Xeva} | R Documentation

## Plot batch data

### Description

Plot data for a batch.id, experiment design or model.id

### Usage

    plotPDX(object, batch = NULL, patient.id = NULL, drug = NULL,
      model.id = NULL, model.color = NULL, control.name = NULL,
      max.time = NULL, treatment.only = FALSE, vol.normal = FALSE,
      impute.value = TRUE, concurrent.time = FALSE,
      control.col = "#e41a1c", treatment.col = "#377eb8", title = "",
      xlab = "Time", ylab = "Volume", log.y = FALSE, SE.plot = c("all",
      "none", "errorbar", "ribbon"), aspect.ratio = c(1, NULL),
      minor.line.size = 0.5, major.line.size = 0.7)

    plotBatch(object, batch = NULL, patient.id = NULL, drug = NULL,
      control.name = NULL, max.time = NULL, treatment.only = FALSE,
      vol.normal = FALSE, impute.value = TRUE, concurrent.time = FALSE,
      control.col = "#6baed6", treatment.col = "#fc8d59", title = "",
      xlab = "Time", ylab = "Volume", log.y = FALSE, SE.plot = c("all",
      "none", "errorbar", "ribbon"), aspect.ratio = c(1, NULL),
      minor.line.size = 0.5, major.line.size = 0.7)

### Arguments

`object` | Xeva object.
`batch` | Batch name or experiment design list.
`patient.id` | Patient id from the `XevaSet`. Default `NULL`.
`drug` | Name of the drug. Default `NULL`.
`model.id` | One or multiple model.id. Default `NULL`.
`model.color` | Color for `model.id`. Default `NULL`.
`control.name` | Name of the control sample.
`max.time` | Maximum time point of the plot. Default `NULL` will plot complete data.
`treatment.only` | Default `FALSE`. Given full data `treatment.only=TRUE` will plot data only during treatment.
`vol.normal` | Default `FALSE`. If `TRUE`, volume will be normalized.
`impute.value` | Default `TRUE` will impute values if missing.
`concurrent.time` | Default `FALSE`. If `TRUE`, cut the batch data such that control and treatment will end at the same time point.
`control.col` | Color for control plots.
`treatment.col` | Color for treatment plots.
`title` | Title of the plot.
`xlab` | Title of the x-axis.
`ylab` | Title of the y-axis.
`log.y` | Default `FALSE`. If `TRUE`, y-axis will be log-transformed.
`SE.plot` | Plot type. Default `"all"` will plot all plots and average curves. Possible values are `"all"`, `"none"`, `"errorbar"`, and `"ribbon"`.
`aspect.ratio` | Default `1` will create a plot of equal width and height.
`minor.line.size` | Line size for minor lines. Default `0.5`.
`major.line.size` | Line size for major lines. Default `0.7`.

### Value

A ggplot2 plot with control and treatment batch data.

### Examples

    data(brca)
    plotPDX(brca, model.id=c("X.6047.LJ16","X.6047.LJ16.trab"))

    plotPDX(brca, batch="X-1004.BGJ398", vol.normal=TRUE)
    expDesign <- list(batch.name="myBatch", treatment=c("X.6047.LJ16","X.6047.LJ16.trab"),
                 control=c("X.6047.uned"))
    plotBatch(brca, batch=expDesign, vol.normal=TRUE)
    plotBatch(brca, batch=expDesign, vol.normal=FALSE, SE.plot = "errorbar")

[Package Xeva version 1.3.0 Index]