plotIt: All-in-one plot function for blotIt
In JetiLab/blotIt: Software set for alignment of biological replicate data

View source: R/02_exported_functions.R

plotIt

R 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'.