Visualise registration results

Usage

# S3 method for res_greatR
plot(
  x,
  type = c("result", "original"),
  genes_list = NULL,
  show_rep_mean = FALSE,
  ncol = NULL,
  title = NULL,
  ...
)

# S3 method for dist_greatR
plot(
  x,
  type = c("result", "original"),
  match_timepoints = TRUE,
  title = NULL,
  ...
)

# S3 method for summary.res_greatR
plot(
  x,
  type = c("all", "registered"),
  type_dist = c("histogram", "density"),
  genes_list = NULL,
  bins = 30,
  alpha = NA,
  scatterplot_size = c(4, 3),
  title = NULL,
  ...
)

Arguments

x

Input object.

For plot.res_greatR(): registration results, output of the register() registration process.
For plot.summary.res_greatR(): registration results summary, output of summary().
For plot.dist_greatR(): pairwise distances between reference and query time points, output of calculate_distance().

type

Type of plot.

For both plot.res_greatR() and plot.dist_greatR(): whether to use registration "result" (default) or "original" time points.
For plot.summary.res_greatR(): whether to show "all" genes (default) or only "registered" ones.

genes_list

Optional vector indicating the gene_id values to be plotted.

show_rep_mean

Whether to show replicate mean values.

ncol

Number of columns in the plot grid. By default this is calculated automatically.

title

Optional plot title.

...

Arguments to be passed to methods (ignored).

match_timepoints

If TRUE, will match query time points to reference time points.

type_dist

Type of marginal distribution. Can be either "histogram" (default), or "density".

bins

Number of bins to use when type_dist = "histogram". By default, 30.

alpha

Optional opacity of the points in the scatterplot.

scatterplot_size

Vector c(width, height) specifying the ratio of width and height of the scatterplot with respect to stretch and shift distribution plots.

Value

For plot.res_greatR(): plot of genes of interest after registration process (type = "result") or showing original time points (type = "original").
For plot.dist_greatR(): distance heatmap of gene expression profiles over time between reference and query.
For plot.summary.res_greatR(): TODO.