fisher_scatterplot: Plot results of gene frequency Fisher's exact test.

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

Plot results of gene frequency Fisher's exact test.

Description

Plots results of Fisher's exact test on gene frequency obtained via gene_frequency_fisher() as a scatterplot.

Usage

fisher_scatterplot(
  fisher_df,
  p_value_col = "Fisher_p_value_fdr",
  annot_threshold = 0.05,
  annot_color = "red",
  gene_sym_col = "GeneName",
  do_not_highlight = NULL,
  keep_not_highlighted = TRUE
)

Arguments

fisher_df	Test results obtained via gene_frequency_fisher()
p_value_col	Name of the column containing the p-value to consider
annot_threshold	Annotate with a different color if a point is below the significance threshold. Single numerical value.
annot_color	The color in which points below the threshold should be annotated
gene_sym_col	The name of the column containing the gene symbol
do_not_highlight	Either NULL, a character vector, an expression or a purrr-style lambda. Tells the function to ignore the highlighting and labeling of these genes even if their p-value is below the threshold. See details.
keep_not_highlighted	If present, how should not highlighted genes be treated? If set to TRUE points are plotted and colored with the chosen color scale. If set to FALSE the points are removed entirely from the plot.

Details

Specifying genes to avoid highlighting

In some cases, users might want to avoid highlighting certain genes even if their p-value is below the threshold. To do so, use the argument do_not_highlight: character vectors are appropriate for specific genes that are to be excluded, expressions or lambdas allow a finer control. For example we can supply:

expr <- rlang::expr(!stringr::str_starts(GeneName, "MIR") &
                      average_TxLen_1 >= 300)

with this expression, genes that have a p-value < threshold and start with "MIR" or have an average_TxLen_1 lower than 300 are excluded from the highlighted points. NOTE: keep in mind that expressions are evaluated inside a dplyr::filter context.

Similarly, lambdas are passed to the filtering function but only operate on the column containing the gene symbol.

lambda <- ~ stringr::str_starts(.x, "MIR")

Value

A plot

See Also

Other Plotting functions: CIS_volcano_plot(), HSC_population_plot(), circos_genomic_density(), 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")
)
cis <- CIS_grubbs(aggreg, by = "SubjectID")
fisher <- gene_frequency_fisher(cis$cis$PT001, cis$cis$PT002,
    min_is_per_gene = 2
)
fisher_scatterplot(fisher)

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