CIS_volcano_plot: Trace volcano plot for computed CIS data.

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

Trace volcano plot for computed CIS data.

Description

Traces a volcano plot for IS frequency and CIS results.

Usage

CIS_volcano_plot(
  x,
  onco_db_file = "proto_oncogenes",
  tumor_suppressors_db_file = "tumor_suppressors",
  species = "human",
  known_onco = known_clinical_oncogenes(),
  suspicious_genes = clinical_relevant_suspicious_genes(),
  significance_threshold = 0.05,
  annotation_threshold_ontots = 0.1,
  highlight_genes = NULL,
  title_prefix = NULL,
  return_df = FALSE
)

Arguments

x	Either a simple integration matrix or a data frame resulting from the call to CIS_grubbs with add_standard_padjust = TRUE
onco_db_file	Uniprot file for proto-oncogenes (see details). If different from default, should be supplied as a path to a file.
tumor_suppressors_db_file	Uniprot file for tumor-suppressor genes. If different from default, should be supplied as a path to a file.
species	One between "human", "mouse" and "all"
known_onco	Data frame with known oncogenes. See details.
suspicious_genes	Data frame with clinical relevant suspicious genes. See details.
significance_threshold	The significance threshold
annotation_threshold_ontots	Value above which genes are annotated with colorful labels
highlight_genes	Either NULL or a character vector of genes to be highlighted in the plot even if they're not above the threshold
title_prefix	A string or character vector to be displayed in the title - usually the project name and other characterizing info. If a vector is supplied, it is concatenated in a single string via paste()
return_df	Return the data frame used to generate the plot? This can be useful if the user wants to manually modify the plot with ggplot2. If TRUE the function returns a list containing both the plot and the data frame.

Details

Input data frame

Users can supply as x either a simple integration matrix or a data frame resulting from the call to CIS_grubbs. In the first case an internal call to the function CIS_grubbs() is performed.

Oncogene and tumor suppressor genes files

These files are included in the package for user convenience and are simply UniProt files with gene annotations for human and mouse. For more details on how this files were generated use the help ?tumor_suppressors, ?proto_oncogenes

Known oncogenes

The default values are included in this package and it can be accessed by doing:

known_clinical_oncogenes()

If the user wants to change this parameter the input data frame must preserve the column structure. The same goes for the suspicious_genes parameter (DOIReference column is optional):

clinical_relevant_suspicious_genes()

Value

A plot or a list containing a plot and a data frame

Required tags

The function will explicitly check for the presence of these tags:

• gene_symbol

See Also

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

Examples

data("integration_matrices", package = "ISAnalytics")
cis_plot <- CIS_volcano_plot(integration_matrices,
    title_prefix = "PJ01"
)
cis_plot

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