plot_align_me: All-in-one plot function for blotIt3

In SeverinBang/blotIt3: Software set for alignment of biological replicate data

All-in-one plot function for blotIt3

Description

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

Usage

plot_align_me(
  out_list,
  ...,
  plot_points = "aligned",
  plot_line = "aligned",
  spline = FALSE,
  scales = "free",
  align_zeros = TRUE,
  plot_caption = TRUE,
  ncol = NULL,
  my_colors = NULL,
  duplicate_zero_points = FALSE,
  my_order = NULL,
  plot_scale_y = NULL,
  plot_scale_x = NULL,
  dose_response = FALSE,
  x_lab = NULL,
  y_lab = NULL
)

Arguments

out_list	out_list file as produced by align_me, a list of data.frames.
...	Logical expression used for subsetting the data frames, e.g. name == "pERK1" & time < 60. To reproduce the known function plot1, plot2 and plot3, use: plot1 plot_points = 'original', plot_line = 'prediction' plot2 plot_points = 'scaled', plot_line = 'aligned' plot3 plot_points = 'aligned', plot_line = 'aligned'
plot_points	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").
plot_line	Same as above but with a line and error band.
spline	Logical, if set to TRUE, what is specified as plot_line will be plotted as a smooth spline instead of straight lines between points.
scales	String passed as scales argument to facet_wrap.
align_zeros	Logical, if TRUE, the zero ticks are aligned between the facets.
plot_caption	Logical, if TRUE, a caption describing the plotted data is added to the plot.
ncol	Numerical passed as ncol argument to facet_wrap.
my_colors	list of custom color values as taken by the values argument in the scale_color_manual method for ggplot objects.
duplicate_zero_points	Logical, if set to TRUE all zero time points are assumed to belong to the first condition. E.g. when the different conditions consist of treatments added at time zero. Default is FALSE.
my_order	Optional list of target names in the custom order that will be used for faceting.
plot_scale_y	character, defining the scale of the y axis
plot_scale_x	character, defining the scale of the x axis
dose_response	Logical, indicates if the plot should be dose response
x_lab	Optional, value passed to xlab parameter of ggplot for the x-axis. Default is NULL leading to 'Time' or 'Dose', respectively.
y_lab	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

SeverinBang/blotIt3 documentation built on April 4, 2022, 5 a.m.