scPhyloX.tools.utils

Functions

corr_plot(x, y, ax[, stats, r0_x, r0_y, r1_x, r1_y, ...])	Draw a scatter plot of the two sets of data and show their correlation coefficients
colless_index(tree)	calculate Colless' index
colless_index_corrected(tree)	calculate corrected Colless' index
ext_gen(cell)	Extract generation with given cell name
ext_cid(cell)	Extract cell id with given cell name
reconstruct(lineage_info, sel_cells[, file_name])	Reconstruct phylogenetic tree of simulation data

Module Contents

corr_plot(x, y, ax, stats='pearson', r0_x=None, r0_y=None, r1_x=None, r1_y=None, line='fit', alternative='two-sided', fontsize=10)

Draw a scatter plot of the two sets of data and show their correlation coefficients

Args:

x:

data1

y:

data2

ax:

axes to draw scatter on

stats:

pearson or spearman

r0_x, r0_y, r1_x, r1_y:

locations to label the correlation coefficient and the p-value

line:

fit or diag, fit for linear regression

alternative:

greater, less or two-sided

fontsize:

fontsize

Return:

matplotlib.axes

colless_index(tree)

calculate Colless’ index

Args:

tree:

Phylogenetic tree

Return:

float:

Colless’ index

colless_index_corrected(tree)

calculate corrected Colless’ index

Args:

tree:

Phylogenetic tree

Return:

float:

corrected Colless’ index

ext_gen(cell)

Extract generation with given cell name

ext_cid(cell)

Extract cell id with given cell name

reconstruct(lineage_info, sel_cells, file_name=None)

Reconstruct phylogenetic tree of simulation data

Args:

lineage_info:

system.lineage_info

sel_cells:

cells to build phylogenetic tree

file_name:

path to save tree. if None, just return

Return:

text newick tree