plot_all_charts: Plot a set of charts representing allele frequencies and...

In robjohnnoble/demonanalysis: Analysis and plotting of demon data

Description

Plot a set of charts representing allele frequencies and genotype sizes

Usage

plot_all_charts(path_or_dflist, output_filename = NA,
  file_type = "png", output_dir = NA, max_size = NA,
  generation = NA, numcells = NA, max_count = 10,
  num_parameters = NA)

Arguments

path_or_dflist	folder containing the input files, or a list of data frames
output_filename	name of output image file
file_type	either "pdf" or "png" (other values default to "pdf")
output_dir	folder in which to save the image file; if NA then plots are displayed on screen instead
max_size	maximum size (default NA corresponds to plotting frequencies, not sizes)
generation	Generation at which to make the measurement (default NA corresponds to the final Generation)
numcells	Number of cells at which to make the measurement (default NA corresponds to the final size)
max_count	Max value of y-axis in counts plot
num_parameters	Number of parameters, accounting for the first set of columns in the dataframe

Details

If both generation and numcells are provided then numcells takes precedent. A value for num_parameters is required only if the input data represents multiple simulations and either generation or numcells is specified.

Value

plot displyed on screen

Examples

plot_all_charts(system.file("extdata", "", package = "demonanalysis", mustWork = TRUE))
plot_all_charts(list(output_allele_counts, output_driver_allele_counts, 
output_genotype_counts, output_driver_genotype_counts))

# combining results from multiple simulations:
df1 <- all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "allele_counts", generation = 10)
df2 <- all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "driver_allele_counts", generation = 10)
df3 <- all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "genotype_counts", generation = 10)
df4 <- all_output(system.file("example_batch", "", package = "demonanalysis", mustWork = TRUE), 
df_type = "driver_genotype_counts", generation = 10)
num_parameters <- count_parameters(system.file("example_batch", "", 
package = "demonanalysis", mustWork = TRUE))
plot_all_charts(list(df1, df2, df3, df4), num_parameters = num_parameters)

robjohnnoble/demonanalysis documentation built on June 30, 2020, 12:47 a.m.