Description Usage Arguments Details Value
Computes and plots the Probability Density Function (PDF) of a numeric attribute of a lineage or division tree. The PDF can be plotted for each colony or generation or for the whole population. Each PDF is computed by fitting a distribution model (Normal, Gamma or Lognormal) to the corresponding data.
1 2 3 4 5 |
tree |
The lineage or division tree, an object of class |
treeT |
A character string naming the type of
|
attr |
The name of the attribute in the |
unit |
The unit of |
grouped |
A character string naming the grouping method:
|
groups |
The IDs of the groups for which to plot the PDF, a vector of positive integer values.
This argument is ignored in case |
Ngroups |
Number of colonies in the movie (if |
model |
A character string naming the distribution model to be fitted:
Each model is fitted using the maximum likelyhood estimation (MLE) method
provided by |
plot3D |
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
|
Each PDF is computed considering all cells that are included in the analysis,
as returned from get_cells
,
except for cells with NA
value in attr
.
The range of x-axis (attribute) values depicted in each 2D plot is common and
is calculated as the range of values of all groups specified in groups
.
Color denotes the corresponding group.
A dataframe with the following columns:
group
is the ID of the group (a positive integer value)
or -2
in case grouped = "pop"
.
Ncells
is the number of cells, a positive integer value.
distr
is a character string naming the distribution model that was fitted:
"norm"
for Normal,
"gamma"
for Gamma and
"lnorm"
for Lognormal distribution or
NA
if no distribution was fitted (less than 2 unique values of attr
exist).
mean
is the mu parameter (mean) of the Normal distribution (a numeric value),
or NA
in case distr != "norm"
.
sd
is the sigma parameter (standard deviation) of the Normal distribution (a non-zero positive numeric value),
or NA
in case distr != "norm"
.
shape
is the alpha parameter (shape) of the Gamma distribution (a non-zero positive numeric value),
or NA
in case distr != "gamma"
.
rate
is the beta parameter (rate) of the Gamma distribution (a non-zero positive numeric value),
or NA
in case distr != "gamma"
.
meanlog
is the mu parameter of the Lognormal distribution (a numeric value),
or NA
in case distr != "lnorm"
.
sdlog
is the sigma parameter of the Lognormal distribution (a non-zero positive numeric value),
or NA
in case distr != "lnorm"
.
BIC
is the BIC value of the fitted distribution (a numeric value),
or NA
in case distr = NA
.
dBIC
is a character string summarizing the strength of the chosen distribution model
specified in distr
against the other models with higher BIC values.
Value is NA
in case model != "auto"
or if distr = NA
.
The format of the string is "<dBIC_norm>, <dBIC_gamma>, <dBIC_lnorm>"
.
Each <dBIC_model>
value is rounded.
The larger a <dBIC_model>
value, the stronger the evidence that attribute attr
of the group
follows the chosen distr
distribution against the <model>
distribution.
Values >10
typically indicate strong preference to the chosen distribution.
For groups with distr = NA
, no plot is generated.
In case no cells exist, no plot is generated and NULL
is returned.
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