Error importing matrix

[aspitaleri]

Hi
I am importing the matrix in attach using the example in https://github.com/moshi4/pyCirclize/blob/main/docs/plot_tips.ipynb

matrix_df=pd.read_csv('t.csv',sep='\t')

circos = Circos.initialize_from_matrix(

       matrix_df,
    r_lim=(95, 100),
    space=5,
    cmap="tab10",
    link_kws=dict(ec="black", lw=0.5, direction=1),
)
fig = circos.plotfig()

but I get error:
ZeroDivisionError Traceback (most recent call last)
Cell In [1604], line 1
----> 1 circos = Circos.initialize_from_matrix(
2
3 a.replace(0,1),
4 r_lim=(95, 100),
5 space=5,
6 cmap="tab10",
7 link_kws=dict(ec="black", lw=0.5, direction=1),
8 )
9 fig = circos.plotfig()

File /opt/homebrew/lib/python3.10/site-packages/pycirclize/circos.py:224, in Circos.initialize_from_matrix(matrix, start, end, space, endspace, r_lim, cmap, link_cmap, ticks_interval, order, label_kws, ticks_kws, link_kws)
221 circos = Circos(matrix.to_sectors(), start, end, space=space, endspace=endspace)
222 for sector in circos.sectors:
223 # Plot label, outer track axis & xticks
--> 224 sector.text(sector.name, **label_kws)
225 outer_track = sector.add_track(r_lim)
226 color = name2color[sector.name]

File /opt/homebrew/lib/python3.10/site-packages/pycirclize/sector.py:249, in Sector.text(self, text, x, r, orientation, **kwargs)
246 if x is None:
247 # Get sector center radian position
248 center_x = (self.start + self.end) / 2
--> 249 rad = self.x_to_rad(center_x)
250 else:
251 rad = self.x_to_rad(x)

File /opt/homebrew/lib/python3.10/site-packages/pycirclize/sector.py:193, in Sector.x_to_rad(self, x, ignore_range_error)
191 err_msg = f"{x=} is invalid range of '{self.name}' sector.\n{self}"
192 raise ValueError(err_msg)
--> 193 size_ratio = self.rad_size / self.size
194 x_from_start = x - self.start
195 rad_from_start = x_from_start * size_ratio
ZeroDivisionError: float division by zero

I tried doing matrix_df.replace(0,10) but still same error. Any help?

t.csv

[moshi4]

Hi, @aspitaleri

The error is probably due to the incorrect format of your matrix file (t.csv). The matrix file must have explicit row names.

Below is an example of a Chord Diagram plot using a matrix file.

from pycirclize import Circos
import pandas as pd

# Create 3 x 6 matrix file
row_names = ["F1", "F2", "F3"]
col_names = ["T1", "T2", "T3", "T4", "T5", "T6"]
matrix_data = [
    [4, 14, 13, 17, 5, 2],
    [7, 1, 6, 8, 12, 15],
    [9, 10, 3, 16, 11, 18],
]
matrix_df = pd.DataFrame(matrix_data, index=row_names, columns=col_names)
matrix_df.to_csv("matrix.tsv", sep="\t")

# Plot chord diagram (Use matrix file)
circos = Circos.initialize_from_matrix("matrix.tsv", space=5, cmap="tab10")
circos.savefig("chord_diagram.png")

matrix.tsv

	T1	T2	T3	T4	T5	T6
F1	4	14	13	17	5	2
F2	7	1	6	8	12	15
F3	9	10	3	16	11	18

chord_diagram.png

[aspitaleri]

I see - I will find out what it is the problem. Thanks. Anyway, if a column has all 0, you get similar error. So I will replace 0 with -1 value, should it work?

[moshi4]

if a column has all 0, you get a similar error. so i will replace 0 with -1 value, should it work?

If a row or column has all 0 values, it means that the row or column has no data to be plotted in the Chord Diagram. Therefore, values with all 0 rows or columns should be preliminarily removed from the matrix.

The following is an example of plotting a Chord Diagram after removing only 0 values from the matrix.

from pycirclize import Circos
import pandas as pd

# Create 3 x 6 matrix file (Only 0 row-column exist)
row_names = ["F1", "F2", "F3"]
col_names = ["T1", "T2", "T3", "T4", "T5", "T6"]
matrix_data = [
    [0, 0, 0, 0, 0, 0],
    [0, 1, 6, 8, 12, 15],
    [0, 10, 3, 16, 11, 18],
]
matrix_df = pd.DataFrame(matrix_data, index=row_names, columns=col_names)

# Remove only zero column matrix data
matrix_df = matrix_df.loc[:, ~(matrix_df <= 0).all(axis=0)]
# Remove only zero row matrix data
matrix_df = matrix_df.loc[~(matrix_df <= 0).all(axis=1)]

# Plot chord diagram (Use matrix file)
circos = Circos.initialize_from_matrix(matrix_df, space=5, cmap="tab10")
circos.savefig("chord_diagram.png")

chord_diagram.png