HSC_population_plot {ISAnalytics} | R Documentation |
Plot of the estimated HSC population size for each patient.
HSC_population_plot( estimates, project_name, timepoints = "Consecutive", models = "Mth Chao (LB)" )
estimates |
The estimates data frame, obtained via
|
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) |
A plot
Other Plotting functions:
CIS_volcano_plot()
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)