Description Usage Arguments Details Value
Computes and plots the growth curves of cell counts (number of cells) in a lineage tree. The growth curve can be plotted for each colony or for the whole population. Each growth curve is computed by fitting the Baranyi and Roberts model to the corresponding data.
1 2 3 |
LT |
The lineage tree, an object of class |
DT |
The corresponding division tree of the |
cols |
The IDs of the colonies for which to fit the Baranyi and Roberts model,
a vector of non-zero positive integer values.
The default value |
Ncols |
Number of colonies in the movie, a non-zero positive integer value.
This argument is ignored in case |
Nframes |
Number of frames in the movie, a non-zero positive integer value. |
frameR |
Frame rate of the movie in frames per minute, a non-zero positive numeric value. |
showRaw |
A logical value ( |
save |
A logical value ( |
savePars |
A named list specifying the parameters of each generated image file.
This argument is ignored in case
|
The parameters of the Baranyi and Roberts model are found using the
non-linear least squares method provided by nls
,
considering all non-root cells, as returned from get_cells
.
When cols = -1
, a common plot for all colonies is generated.
In other cases, a separate plot for each colony specified in cols
is generated.
x-axis represents the time in hours from the start (value 0
) to end of the movie.
y-axis represents the cell counts in logarithmic scale.
The range of y-axis values depicted in each plot is common and
is calculated as the range of values of all specified colonies,
with minimum upper limit 2
(i.e. 20 cells).
Color denotes the corresponding colony.
A dataframe with the following columns:
colony
is the colony ID (a non-zero positive integer value)
or -2
in case cols = -2
.
lag
is the lambda parameter (lag time)
of the Baranyi and Roberts model in hours (a non-zero positive numeric value)
or NA
in case the model failed to be fitted or colony
has only cells which have not been divided.
mumax
is the mumax parameter (maximum specific growth rate)
of the Baranyi and Roberts model in 1/hour (a non-zero positive numeric value)
or NA
in case the model failed to be fitted or colony
has only cells which have not been divided.
For groups with lag = NA
, no plot is generated, except for the case that showRaw = TRUE
.
In case no cells exist, no plot is generated and NULL
is returned.
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