Trace volcano plot for computed CIS data.

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.

Value

A plot or a list containing a plot and a 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:

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):

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"
)
#> Calculating CIS_grubbs for x...
#> Warning: Warning: missing genes in refgenes table
#> ℹ A total of 5 genes were found in the input data but not in the refgene table. This may be caused by a mismatch in the annotation phase of the matrix. Here is a summary: 
#>     GeneName GeneStrand chr
#> 1:    CRELD2          -  15
#> 2:      HTR4          +   6
#> 3:    UBE2D2          +  16
#> 4: LINC01133          +  19
#> 5:  PLEKHG4B          -  14
#> ℹ NOTE: missing genes will be removed from the final output! Review results carefully
#> ℹ A total of 25 IS will be removed because of missing genes ( 1.48 % of total IS in input)
#> Loading annotated genes -  species selected: 
#> • Homo sapiens (Human)
#> Loading annotated genes -  done
cis_plot