plot_connections: Plot connections

In cicero: Precict cis-co-accessibility from single-cell chromatin accessibility data

Description

Plotting function for Cicero connections. Uses plotTracks as its basis

Usage

plot_connections(
  connection_df,
  chr,
  minbp,
  maxbp,
  coaccess_cutoff = 0,
  peak_color = "#B4656F",
  connection_color = "#7F7CAF",
  connection_color_legend = TRUE,
  alpha_by_coaccess = FALSE,
  connection_width = 2,
  connection_ymax = NULL,
  gene_model = NULL,
  gene_model_color = "#81D2C7",
  gene_model_shape = c("smallArrow", "box"),
  comparison_track = NULL,
  comparison_coaccess_cutoff = 0,
  comparison_peak_color = "#B4656F",
  comparison_connection_color = "#7F7CAF",
  comparison_connection_color_legend = TRUE,
  comparison_connection_width = 2,
  comparison_ymax = NULL,
  collapseTranscripts = FALSE,
  include_axis_track = TRUE,
  return_as_list = FALSE,
  viewpoint = NULL,
  comparison_viewpoint = TRUE,
  viewpoint_color = "#F0544F",
  viewpoint_fill = "#EFD8D7",
  viewpoint_alpha = 0.5
)

Arguments

connection_df	Data frame of connections, which must include the columns 'Peak1', 'Peak2', and 'coaccess'. Generally, the output of run_cicero or assemble_connections.
chr	The chromosome of the region you would like to plot in the form 'chr10'.
minbp	The base pair coordinate of the start of the region to be plotted.
maxbp	The base pair coordinate of the end of the region to be plotted.
coaccess_cutoff	The minimum cicero co-accessibility score you would like to be plotted. Default is 0.
peak_color	Color for peak annotations - a single color, the name of a column containing color values that correspond to Peak1, or the name of column containing a character or factor to base peak colors on.
connection_color	Color for connection lines. A single color, the name of a column containing color values, or the name of a column containing a character or factor to base connection colors on.
connection_color_legend	Logical, should connection color legend be shown?
alpha_by_coaccess	Logical, should the transparency of connection lines be scaled based on co-accessibility score?
connection_width	Width of connection lines.
connection_ymax	Connection y-axis height. If NULL, chosen automatically.
gene_model	Either NULL or a data.frame. The data.frame should be in a form compatible with the Gviz function GeneRegionTrack-class (cannot have NA as column names).
gene_model_color	Color for gene annotations.
gene_model_shape	Shape for gene models, passed to GeneRegionTrack-class. Options described at GeneRegionTrack-class.
comparison_track	Either NULL or a data frame. If a data frame, a second track of connections will be plotted based on this data. This data frame has the same requirements as connection_df (Peak1, Peak2 and coaccess columns).
comparison_coaccess_cutoff	The minimum cicero co-accessibility score you would like to be plotted for the comparison dataset. Default = 0.
comparison_peak_color	Color for comparison peak annotations - a single color, the name of a column containing color values that correspond to Peak1, or the name of a column containing a character or factor to base peak colors on.
comparison_connection_color	Color for comparison connection lines. A single color, the name of a column containing color values, or the name of a column containing a character or factor to base connection colors on.
comparison_connection_color_legend	Logical, should comparison connection color legend be shown?
comparison_connection_width	Width of comparison connection lines.
comparison_ymax	Connection y-axis height for comparison track. If NULL, chosen automatically.
collapseTranscripts	Logical or character scalar. Can be one in gene, longest, shortest or meta. Variable is passed to the GeneRegionTrack-class function of Gviz. Determines whether and how to collapse related transcripts. See Gviz documentation for details.
include_axis_track	Logical, should a genomic axis be plotted?
return_as_list	Logical, if TRUE, the function will not plot, but will return the plot components as a list. Allows user to add/customize Gviz components and plot them separately using plotTracks.
viewpoint	NULL or Coordinates in form "chr1_10000_10020". Use viewpoint if you would like to plot cicero connections "4C-seq style". Only connections originating in the viewpoint will be shown. Ideal for comparisons with 4C-seq data. If comparison_viewpoint is TRUE, any comparison track will be subsetted as well.
comparison_viewpoint	Logical, should viewpoint apply to comparison track as well?
viewpoint_color	Color for the highlight border.
viewpoint_fill	Color for the highlight fill.
viewpoint_alpha	Alpha value for the highlight fill.

Value

A gene region plot, or list of components if return_as_list is TRUE.

Examples

  cicero_cons <- data.frame(
             Peak1 = c("chr18_10034652_10034983", "chr18_10034652_10034983",
                       "chr18_10034652_10034983", "chr18_10034652_10034983",
                       "chr18_10087586_10087901", "chr18_10120685_10127115",
                       "chr18_10097718_10097934", "chr18_10087586_10087901",
                       "chr18_10154818_10155215", "chr18_10238762_10238983",
                       "chr18_10198959_10199183", "chr18_10250985_10251585"),
             Peak2 = c("chr18_10097718_10097934", "chr18_10087586_10087901",
                       "chr18_10154818_10155215", "chr18_10238762_10238983",
                       "chr18_10198959_10199183", "chr18_10250985_10251585",
                       "chr18_10034652_10034983", "chr18_10034652_10034983",
                       "chr18_10034652_10034983", "chr18_10034652_10034983",
                       "chr18_10087586_10087901", "chr18_10120685_10127115"),
             coaccess = c(0.0051121787, 0.0016698617, 0.0006570246,
                          0.0013466927, 0.0737935011, 0.3264019452,
                          0.0051121787, 0.0016698617, 0.0006570246,
                          0.0013466927, 0.0737935011, 0.3264019452))
  plot_connections(cicero_cons, chr = "chr18",
                   minbp = 10034652,
                   maxbp = 10251585,
                   peak_color = "purple")

cicero documentation built on Dec. 10, 2020, 2 a.m.