- Language: en
METHOD_OPTIONS¶
Type: dict_record
method options for plt_grph
Example:-
METHOD_OPTIONS:
py_module: grph
py_module¶
Type: one_of(grph)
Python module required to process this script file
Example:-
py_module: grph
FILE_PATHS¶
Type: dict_record
file paths
Example:-
FILE_PATHS:
output_folder: auto
output_file_ext: ['svg']
solutions:
orig: ./path_to_input_solution.pyml
final: ./path_to_final_solution.pyml
output_folder¶
Type: output_folder / auto
Output folder - results of computation stored here
Example:-
output_folder: auto
output_file_ext¶
Type: list_of(pdf,png,svg)
Output file extension - determines graphical output file format.
Example:-
output_file_ext: ['svg']
DATA_FIELDS¶
Type: dict_record
data fields for popy.dat.fields object
Example:-
DATA_FIELDS:
type_field: TYPE
id_field: ID
time_field: TIME
type_field¶
Type: str
Field name in data file that contains row type info, e.g. obs/dose etc
Example:-
type_field: TYPE
OUTPUT_GRAPHS¶
Type: list_record
List of graphs to output.
Example:-
OUTPUT_GRAPHS:
- FE_BAR_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
scaling: prop
orientation: vertical
- COMB_SPAG_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
- RE_SPIDER_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
scaling: prop
options_list: []
- SPAG_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
- COMB_QUANT_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
quantile_list: [0.05, 0.5, 0.95]
bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
min_bin_count: 10
- GRID_SPAG_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
n_columns: 3
FE_BAR_GRPH¶
Type: dict_record
Plot bar chart of f[X] values.
Example:-
FE_BAR_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
scaling: prop
orientation: vertical
y_axis_label_list¶
Type: list(str)
List of labels for y variables that appear on axes.
Example:-
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list¶
Type: list(str)
List of y variable types, orig = original data set sim = simulated data
Example:-
y_var_src_list: ['orig', 'sim']
y_var_label_list¶
Type: list(str)
List of y variable labels, which appear in the legend.
Example:-
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list¶
Type: list(str)
List of colours for y variable plot lines.
Example:-
y_var_colour_list: ['b', 'g']
y_var_symbol_list¶
Type: list(str)
List of plot line styles for y variable plot lines.
Example:-
y_var_symbol_list: ['-', '-']
single_file¶
Type: bool
Render to a single file where possible (PDF only)
Example:-
single_file: False
orientation¶
Type: one_of(vertical,horizontal)
Orientation of the bars.
Example:-
orientation: vertical
COMB_SPAG_GRPH¶
Type: dict_record
Plot data for all individuals on one graph.
Example:-
COMB_SPAG_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
y_axis_label_list¶
Type: list(str)
List of labels for y variables that appear on axes.
Example:-
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list¶
Type: list(str)
List of y variable types, orig = original data set sim = simulated data
Example:-
y_var_src_list: ['orig', 'sim']
y_var_label_list¶
Type: list(str)
List of y variable labels, which appear in the legend.
Example:-
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list¶
Type: list(str)
List of colours for y variable plot lines.
Example:-
y_var_colour_list: ['b', 'g']
y_var_symbol_list¶
Type: list(str)
List of plot line styles for y variable plot lines.
Example:-
y_var_symbol_list: ['-', '-']
single_file¶
Type: bool
Render to a single file where possible (PDF only)
Example:-
single_file: False
x_scale¶
Type: one_of(linear,log)
x axis scale - can be either ‘linear’ or ‘log’.
Example:-
x_scale: linear
y_var_list¶
Type: list(str)
List of y variable names to be plotted on graph.
Example:-
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list¶
Type: list(str)
List of scales (linear or log) for multiple y axes.
Example:-
y_scale_list: ['linear', 'log']
options_list¶
Type: list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy)
List of visual options to apply to individual plots.
Example:-
options_list: ['legend', 'grid', 'dose_lines']
RE_SPIDER_GRPH¶
Type: dict_record
Plot data on separate graphs for each individual.
Example:-
RE_SPIDER_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
scaling: prop
options_list: []
y_axis_label_list¶
Type: list(str)
List of labels for y variables that appear on axes.
Example:-
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list¶
Type: list(str)
List of y variable types, orig = original data set sim = simulated data
Example:-
y_var_src_list: ['orig', 'sim']
y_var_label_list¶
Type: list(str)
List of y variable labels, which appear in the legend.
Example:-
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list¶
Type: list(str)
List of colours for y variable plot lines.
Example:-
y_var_colour_list: ['b', 'g']
y_var_symbol_list¶
Type: list(str)
List of plot line styles for y variable plot lines.
Example:-
y_var_symbol_list: ['-', '-']
single_file¶
Type: bool
Render to a single file where possible (PDF only)
Example:-
single_file: False
options_list¶
Type: list_of(overlay)
List of visual options to apply to individual plots.
Example:-
options_list: []
SPAG_GRPH¶
Type: dict_record
Plot data for each individual.
Example:-
SPAG_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
y_axis_label_list¶
Type: list(str)
List of labels for y variables that appear on axes.
Example:-
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list¶
Type: list(str)
List of y variable types, orig = original data set sim = simulated data
Example:-
y_var_src_list: ['orig', 'sim']
y_var_label_list¶
Type: list(str)
List of y variable labels, which appear in the legend.
Example:-
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list¶
Type: list(str)
List of colours for y variable plot lines.
Example:-
y_var_colour_list: ['b', 'g']
y_var_symbol_list¶
Type: list(str)
List of plot line styles for y variable plot lines.
Example:-
y_var_symbol_list: ['-', '-']
single_file¶
Type: bool
Render to a single file where possible (PDF only)
Example:-
single_file: False
x_scale¶
Type: one_of(linear,log)
x axis scale - can be either ‘linear’ or ‘log’.
Example:-
x_scale: linear
y_var_list¶
Type: list(str)
List of y variable names to be plotted on graph.
Example:-
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list¶
Type: list(str)
List of scales (linear or log) for multiple y axes.
Example:-
y_scale_list: ['linear', 'log']
options_list¶
Type: list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy,overlay)
List of visual options to apply to individual plots.
Example:-
options_list: ['legend', 'grid', 'dose_lines']
COMB_QUANT_GRPH¶
Type: dict_record
Plot orig and simulation data using histograms on one graph.
Example:-
COMB_QUANT_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
quantile_list: [0.05, 0.5, 0.95]
bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
min_bin_count: 10
y_axis_label_list¶
Type: list(str)
List of labels for y variables that appear on axes.
Example:-
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list¶
Type: list(str)
List of y variable types, orig = original data set sim = simulated data
Example:-
y_var_src_list: ['orig', 'sim']
y_var_label_list¶
Type: list(str)
List of y variable labels, which appear in the legend.
Example:-
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list¶
Type: list(str)
List of colours for y variable plot lines.
Example:-
y_var_colour_list: ['b', 'g']
y_var_symbol_list¶
Type: list(str)
List of plot line styles for y variable plot lines.
Example:-
y_var_symbol_list: ['-', '-']
single_file¶
Type: bool
Render to a single file where possible (PDF only)
Example:-
single_file: False
x_scale¶
Type: one_of(linear,log)
x axis scale - can be either ‘linear’ or ‘log’.
Example:-
x_scale: linear
y_var_list¶
Type: list(str)
List of y variable names to be plotted on graph.
Example:-
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list¶
Type: list(str)
List of scales (linear or log) for multiple y axes.
Example:-
y_scale_list: ['linear', 'log']
options_list¶
Type: list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy)
List of visual options to apply to individual plots.
Example:-
options_list: ['legend', 'grid', 'dose_lines']
quantile_list¶
Type: list(float)
List of quantiles to plot for each bin of the histogram.
Example:-
quantile_list: [0.05, 0.5, 0.95]
bin_indexer¶
Type: one_of_record
Possible bin indexing methods.
Example:-
bin_indexer:
EQUAL_SPACE: {n_bins: auto}
UNEQUAL_SPACE¶
Type: dict_record
fixed, irregularly spaced user defined bin edges.
Example:-
UNEQUAL_SPACE:
bin_edge_list: [2.0, 4.0, 8.0]
bin_edge_list¶
Type: list(float)
List of user-defined bin edges.
Example:-
bin_edge_list: [2.0, 4.0, 8.0]
K_MEANS¶
Type: dict_record
Deduce bin centres automatically using k-means algorithm for a pre-determined number of bins.
Example:-
K_MEANS:
n_bins: 10
init_method: random
init_method¶
Type: one_of(random)
Initialisation method for k-means algorithm.
Example:-
init_method: random
GRID_SPAG_GRPH¶
Type: dict_record
Plot data for all individuals on one graph.
Example:-
GRID_SPAG_GRPH:
graph_title: My rather excellent graph
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list: ['orig', 'sim']
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list: ['b', 'g']
y_var_symbol_list: ['-', '-']
rows_per_page: 1
columns_per_page: 1
single_file: False
x_var: TIME
x_axis_label: Time (hours)
x_scale: linear
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list: ['linear', 'log']
options_list: ['legend', 'grid', 'dose_lines']
n_columns: 3
y_axis_label_list¶
Type: list(str)
List of labels for y variables that appear on axes.
Example:-
y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
y_var_src_list¶
Type: list(str)
List of y variable types, orig = original data set sim = simulated data
Example:-
y_var_src_list: ['orig', 'sim']
y_var_label_list¶
Type: list(str)
List of y variable labels, which appear in the legend.
Example:-
y_var_label_list: ['drug in plasma', 'bio marker in plasma']
y_var_colour_list¶
Type: list(str)
List of colours for y variable plot lines.
Example:-
y_var_colour_list: ['b', 'g']
y_var_symbol_list¶
Type: list(str)
List of plot line styles for y variable plot lines.
Example:-
y_var_symbol_list: ['-', '-']
single_file¶
Type: bool
Render to a single file where possible (PDF only)
Example:-
single_file: False
x_scale¶
Type: one_of(linear,log)
x axis scale - can be either ‘linear’ or ‘log’.
Example:-
x_scale: linear
y_var_list¶
Type: list(str)
List of y variable names to be plotted on graph.
Example:-
y_var_list: ['CONC_DRUG', 'CONC_BIO_MARKER']
y_scale_list¶
Type: list(str)
List of scales (linear or log) for multiple y axes.
Example:-
y_scale_list: ['linear', 'log']
options_list¶
Type: list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy)
List of visual options to apply to individual plots.
Example:-
options_list: ['legend', 'grid', 'dose_lines']