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]