usage: pcdl_plot_timeseries [-h] [--custom_data_type [CUSTOM_DATA_TYPE ...]]
[--microenv MICROENV] [--physiboss PHYSIBOSS]
[--settingxml SETTINGXML] [-v VERBOSE]
[--frame FRAME] [--cat_drop [CAT_DROP ...]]
[--cat_keep [CAT_KEEP ...]] [--z_slice Z_SLICE]
[--logy LOGY] [--ylim YLIM [YLIM ...]]
[--secondary_y SECONDARY_Y [SECONDARY_Y ...]]
[--subplots SUBPLOTS] [--sharex SHAREX]
[--sharey SHAREY] [--linestyle LINESTYLE]
[--linewidth LINEWIDTH] [--cmap CMAP]
[--color COLOR [COLOR ...]] [--grid GRID]
[--legend LEGEND] [--yunit YUNIT] [--title TITLE]
[--figsizepx FIGSIZEPX [FIGSIZEPX ...]]
[--ext EXT] [--figbgcolor FIGBGCOLOR]
[path] [focus_cat] [focus_num] [aggregate_num]
this function to generate a timeseries plot and either returns a matplotlib
figure or an image file (jpeg, png, tiff).
positional arguments:
path path to the PhysiCell output directory. default is . .
focus_cat categorical or boolean data column within dataframe
specified under frame. default is None, which is
total, which is all agents or voxels, no categories.
default is None.
focus_num numerical data column within dataframe specified under
frame. default is None, which is count, agent or voxel
count. default is None.
aggregate_num aggregation function {max, mean, median, min, std,
var} for focus_num data. default is mean.
options:
-h, --help show this help message and exit
--custom_data_type [CUSTOM_DATA_TYPE ...]
parameter to specify custom_data variable types other
than float (namely: int, bool, str) like this
var:dtype myint:int mybool:bool mystr:str . downstream
float and int will be handled as numeric, bool as
Boolean, and str as categorical data. default is an
empty string.
--microenv MICROENV should the microenvironment data be loaded? setting
microenv to False will use less memory and speed up
processing. default is True.
--physiboss PHYSIBOSS
if found, should physiboss state data be extracted and
loaded into the df_cell dataframe? default is True.
--settingxml SETTINGXML
the settings.xml that is loaded, from which the cell
type ID label mapping, is extracted, if this
information is not found in the output xml file. set
to None or False if the xml file is missing! default
is False.
-v VERBOSE, --verbose VERBOSE
setting verbose to False for less text output, while
processing. default is True.
--frame FRAME to specifies the data dataframe. cell: dataframe will
be retrieved through the mcds.get_cell_df function.
conc: dataframe will be retrieved through the
mcds.get_conc_df function. default is cell.
--cat_drop [CAT_DROP ...]
if focus is a categorical attribute, set of category
labels to be dropped for the dataframe. Attention:
when the cat_keep parameter is given, then the
cat_drop parameter has to be an empty string! default
is an empty string.
--cat_keep [CAT_KEEP ...]
if focus is a categorical attribute, set of category
labels to be kept in the dataframe. default is an
empty string.
--z_slice Z_SLICE z-axis position to slice a 2D xy-plain out of the 3D
mesh. if z_slice position numeric but not an exact
mesh center coordinate, then z_slice will be adjusted
to the nearest mesh center value, the smaller one, if
the coordinate lies on a saddle point. if set to None,
the whole domain is taken. default is None.
--logy LOGY if True, then y axis is natural log scaled. default is
False.
--ylim YLIM [YLIM ...]
two floats. y axis min and max value. default is None,
which automatically detects min and max value. default
is None.
--secondary_y SECONDARY_Y [SECONDARY_Y ...]
whether to plot on the secondary y-axis. if a listing
of string, which columns to plot on the secondary
y-axis. default is False.
--subplots SUBPLOTS whether to split the plot into subplots, one per
column. default is False.
--sharex SHAREX in case subplots is True, share x-axis by setting some
x-axis labels to invisible. default is False.
--sharey SHAREY in case subplots is True, share y-axis range and
possibly setting some y-axis labels to invisible.
default is False.
--linestyle LINESTYLE
matplotlib line style {-, --, .-, :} string. default
is - .
--linewidth LINEWIDTH
line width in points, float. default is None.
--cmap CMAP matplotlib colormap string from https://matplotlib.org
/stable/tutorials/colors/colormaps.html . default is
None.
--color COLOR [COLOR ...]
listing of color strings referred to by name, RGB or
RGBA code. default is None.
--grid GRID plot axis grid lines. default is True.
--legend LEGEND if True or reverse, place legend on axis subplots.
default is True.
--yunit YUNIT string to specify y-axis unit. None will not print a
unit on the y-axis. default is None.
--title TITLE title to use for the plot. None will print no title.
default is None.
--figsizepx FIGSIZEPX [FIGSIZEPX ...]
size of the figure in pixels (integer), x y. the given
x and y will be rounded to the nearest even number, to
be able to generate movies from the images. default is
640 480.
--ext EXT output format. possible image formats are jpeg, jpg,
png, tif, and tiff. for retrieving a datafarme file
use csv. default is jpeg.
--figbgcolor FIGBGCOLOR
figure background color. None is transparent (png) or
white (jpeg, tiff). default is None.
homepage: https://github.com/elmbeech/physicelldataloader