plotPDX: Plot batch data

Description Usage Arguments Value Examples

View source: R/plot_functions.R

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
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

1
2
3
4
5
6
7
8
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")

Xeva documentation built on Nov. 8, 2020, 5:56 p.m.