circos_genomic_density: Trace a circos plot of genomic densities.

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Trace a circos plot of genomic densities.

Description

For this functionality the suggested package circlize is required. Please note that this function is a simple wrapper of basic circlize functions, for an in-depth explanation on how the functions work and additional arguments please refer to the official documentation Circular Visualization in R

Usage

circos_genomic_density(
  data,
  gene_labels = NULL,
  label_col = NULL,
  cytoband_specie = "hg19",
  track_colors = "navyblue",
  grDevice = c("png", "pdf", "svg", "jpeg", "bmp", "tiff", "default"),
  file_path = getwd(),
  ...
)

Arguments

data	Either a single integration matrix or a list of integration matrices. If a list is provided, a separate density track for each data frame is plotted.
gene_labels	Either NULL or a data frame in bed format. See details.
label_col	Numeric index of the column of gene_labels that contains the actual labels. Relevant only if gene_labels is not set to NULL.
cytoband_specie	Specie for initializing the cytoband
track_colors	Colors to give to density tracks. If more than one integration matrix is provided as data should be of the same length. Values are recycled if length of track_colors is smaller than the length of the input data.
grDevice	The graphical device where the plot should be traced. default, if executing from RStudio is the viewer.
file_path	If a device other than default is chosen, the path on disk where the file should be saved. Defaults to ⁠{current directory}/circos_plot.{device}⁠.
...	Additional named arguments to pass on to chosen device, circlize::circos.par(), circlize::circos.genomicDensity() and circlize::circos.genomicLabels()

Details

Providing genomic labels

If genomic labels should be plotted alongside genomic density tracks, the user should provide them as a simple data frame in standard bed format, namely chr, start, end plus a column containing the labels. NOTE: if the user decides to plot on the default device (viewer in RStudio), he must ensure there is enough space for all elements to be plotted, otherwise an error message is thrown.

Value

NULL

See Also

Other Plotting functions: CIS_volcano_plot(), HSC_population_plot(), fisher_scatterplot(), integration_alluvial_plot(), sharing_heatmap(), sharing_venn(), top_abund_tableGrob(), top_cis_overtime_heatmap()

Examples

data("integration_matrices", package = "ISAnalytics")
data("association_file", package = "ISAnalytics")
aggreg <- aggregate_values_by_key(
    x = integration_matrices,
    association_file = association_file,
    value_cols = c("seqCount", "fragmentEstimate")
)
by_subj <- aggreg |>
    dplyr::group_by(.data$SubjectID) |>
    dplyr::group_split()
circos_genomic_density(by_subj,
    track_colors = c("navyblue", "gold"),
    grDevice = "default", track.height = 0.1
)

calabrialab/ISAnalytics documentation built on Dec. 10, 2024, 10:50 p.m.