plot_connections {cicero} | R Documentation

## Plot connections

### 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")

[Package cicero version 1.2.0 Index]