HSC_population_plot: Plot of the estimated HSC population size for each patient.

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

Plot of the estimated HSC population size for each patient.

Description

Plot of the estimated HSC population size for each patient.

Usage

HSC_population_plot(
  estimates,
  project_name,
  timepoints = "Consecutive",
  models = "Mth Chao (LB)"
)

Arguments

estimates	The estimates data frame, obtained via HSC_population_size_estimate
project_name	The project name, will be included in the plot title
timepoints	Which time points to plot? One between "All", "Stable" and "Consecutive"
models	Name of the models to plot (as they appear in the column of the estimates)

Value

A plot

See Also

Other Plotting functions: CIS_volcano_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")
data("association_file", package = "ISAnalytics")
aggreg <- aggregate_values_by_key(
    x = integration_matrices,
    association_file = association_file,
    value_cols = c("seqCount", "fragmentEstimate")
)
aggreg_meta <- aggregate_metadata(
    association_file = association_file
)
estimate <- HSC_population_size_estimate(
    x = aggreg,
    metadata = aggreg_meta,
    stable_timepoints = c(90, 180, 360),
    cell_type = "Other"
)
p <- HSC_population_plot(estimate$est, "PJ01")
p

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.