plotPDX: Plot batch data

In bhklab/Xeva: Analysis of patient-derived xenograft (PDX) data

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")

bhklab/Xeva documentation built on Nov. 30, 2024, 3:17 a.m.