sharing_heatmap: Plot IS sharing heatmaps.

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

Plot IS sharing heatmaps.

Description

Displays the IS sharing calculated via is_sharing as heatmaps.

Usage

sharing_heatmap(
  sharing_df,
  show_on_x = "g1",
  show_on_y = "g2",
  absolute_sharing_col = "shared",
  title_annot = NULL,
  plot_relative_sharing = TRUE,
  rel_sharing_col = c("on_g1", "on_union"),
  show_perc_symbol_rel = TRUE,
  interactive = FALSE
)

Arguments

sharing_df	The data frame containing the IS sharing data
show_on_x	Name of the column to plot on the x axis
show_on_y	Name of the column to plot on the y axis
absolute_sharing_col	Name of the column that contains the absolute values of IS sharing
title_annot	Additional text to display in the title
plot_relative_sharing	Logical. Compute heatmaps also for relative sharing?
rel_sharing_col	Names of the columns to consider as relative sharing. The function is going to plot one heatmap per column in this argument.
show_perc_symbol_rel	Logical. Only relevant if plot_relative_sharing is set to TRUE, should the percentage symbol be displayed in relative heatmaps?
interactive	Logical. Requires the package plotly is required for this functionality. Returns the heatmaps as interactive HTML widgets.

Value

A list of plots or widgets

See Also

is_sharing

Other Plotting functions: CIS_volcano_plot(), HSC_population_plot(), circos_genomic_density(), fisher_scatterplot(), integration_alluvial_plot(), 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")
)
sharing <- is_sharing(aggreg,
    minimal = FALSE,
    include_self_comp = TRUE
)
sharing_heatmaps <- sharing_heatmap(sharing_df = sharing)
sharing_heatmaps$absolute
sharing_heatmaps$on_g1
sharing_heatmaps$on_union

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