boaz85/pymuller

Muller plot generation in Python

PyMuller

Muller plot generation in Python.

Installation

pip install pymuller

Usage

from pymuller import muller

muller(populations_df, adjacency_df)

The muller function takes two mandatory arguments:

populations_df: A Pandas dataframe with the following structure:

adjacency_df: A Pandas dataframe containing the population adjacency information. Every strain except the ancestral one must have a row.

Optional arguments:

smoothing_std - To smooth things up, a rolling average with a gaussian kernel is applied to each strain frequencies variable. This parameter can be used to control the degree of smoothness.

ax - an existing Matplotlib axis to plot on.

normalize - Normalize population sizes per generation.

color_by - a Pandas series object, that maps identities (index) to colors (values). Colors are represented by numbers in some arbitrary range. The colormap argument determines the actual color of each identity.

pymuller's Issues

More specific formatting instructions? getting an error when trying to plot

So I assigned all my strains a number, have estimated generation number (only 3 time points right now), and population is the number of individual samples of that strain at that time point. I made sure the dtypes were integers, but I am still getting an error that suggests that they are not. Have any recommendations?

color_by argument

hello, could you please add an example of what the color_by object should look like? I attempted this color_by = pd.Series([.1,.2,.3,.4,.5], index = [' GGTA', ' GGTT',' GACA', ' AACA', ' AATA']). So what are the values of color_by supposed to be? I keep getting errors. Most recent one is TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

My adjacency matrix looks like

adjacency_mat
  Parent Identity
1   GGTA     GGTT
2   GGTA     GACA
3   GGTA     AACA
4   GGTA     AATA

and my population matrix looks like

Generation Identity  Population
0          28     GGTA    0.969828
1          39     GGTA    0.000000
2          53     GGTA    0.000000
3          75     GGTA    0.068991
4          28     GGTT    0.001078
5          39     GGTT    0.000000
6          53     GGTT    0.000000

Required argument "color_by"

Hi! I was wondering what form this df should take? I poked through the code but could not figure out the inteded shape. It seems to need to have as index all the identities, but I am not sure what else.