HSC_population_plot {ISAnalytics}R Documentation

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()

Examples

op <- options("ISAnalytics.widgets" = FALSE, "ISAnalytics.verbose" = FALSE)
path_AF <- system.file("extdata", "ex_association_file.tsv",
    package = "ISAnalytics"
)
root_correct <- system.file("extdata", "fs.zip", package = "ISAnalytics")
root_correct <- unzip_file_system(root_correct, "fs")
association_file <- import_association_file(path_AF, root_correct,
    dates_format = "dmy"
)
aggregated_meta <- aggregate_metadata(association_file)
matrices <- import_parallel_Vispa2Matrices_auto(
    association_file = association_file, root = NULL,
    quantification_type = c("fragmentEstimate", "seqCount"),
    matrix_type = "annotated", workers = 2, matching_opt = "ANY"
)
agg <- aggregate_values_by_key(
    x = matrices,
    association_file = association_file,
    value_cols = "seqCount"
)
estimate <- HSC_population_size_estimate(x = agg,
metadata = aggregated_meta,
stable_timepoints = NULL)
p <- HSC_population_plot(estimate, "PROJECT1")
options(op)
[Package ISAnalytics version 1.2.1 Index]