plotIt: All-in-one plot function for blotIt

View source: R/02_exported_functions.R

plotItR Documentation

All-in-one plot function for blotIt

Description

Takes the output of alignReplicates and generates graphs. Which data will be plotted can then be specified separately.

Usage

plotIt(
  inputList,
  ...,
  plotPoints = "aligned",
  plotLine = "aligned",
  spline = FALSE,
  scales = "free",
  alignZeros = TRUE,
  plotCaption = TRUE,
  ncol = NULL,
  useColors = NULL,
  useOrder = NULL,
  plotScaleY = NULL,
  plotScaleX = NULL,
  doseResponse = FALSE,
  doseValueName = "dose",
  labelX = NULL,
  labelY = NULL,
  FacetLabels = c("simple", "full")[1]
)

Arguments

inputList

inputList file as produced by alignReplicates, a list of data.frames.

...

Logical expression used for subsetting the data frames, e.g. name == "pERK1" & time < 60.

plotPoints

String to specify which data set should be plotted in form of points with corresponding error bars. It must be one of c("original", "scaled", "prediction", "aligned").

plotLine

Same as above but with a line and error band.

spline

Logical, if set to TRUE, what is specified as plotLine will be plotted as a smooth spline instead of straight lines between points.

scales

String passed as scales argument to facet_wrap.

alignZeros

Logical, if TRUE, the zero ticks are aligned between the facets.

plotCaption

Logical, if TRUE, a caption describing the plotted data is added to the plot.

ncol

Numerical passed as ncol argument to facet_wrap.

useColors

vector of custom color values as taken by the values argument in the scale_color_manual method for ggplot objects.

useOrder

Optional list of target names in the custom order that will be used for faceting.

plotScaleY

character, defining the scale of the y axis

plotScaleX

character, defining the scale of the x axis

doseResponse

Logical, indicates if the plot should be dose response

doseValueName

name of the column that should be used for the x axis in case of a dose response plot. The default is 'dose'

labelX

Optional, value passed to xlab parameter of ggplot for the x-axis. Default is NULL leading to 'Time' or 'Dose', respectively.

labelY

Optional, value passed to ylab parameter of ggplot for the y-axis. Default is NULL leading to 'Signal'.

Value

ggplot object

Author(s)

Severin Bang and Svenja Kemmer


JetiLab/blotIt documentation built on June 19, 2024, 7:18 a.m.