pyubero / microguilds Goto Github PK

It would be nice that every implementation of several functions can be visualized at the same time. Things to consider:

• there's an obvious limitation of how many bars and colors fill in a radial plot...
• Are radial plots the best way to compare not a single guild pattern, but different guilds?

It would be nice to be able to order the appaerance of the implementations or clusters in the radial plots.

A major update can consist of a new module for computing, generating and displaying several suitable statistical tests for compositional analysis.

It would be interesting to compare the sum of abundance values with the k-values. In order to do that in contexts with very different number of samples, we should add another column with Abudance / n samples.

I rewrite the modify_mastertable.py module to generate a master_tab with 4 context (instead of depth, latitude). I'm getting this error in guild_tensor_generate.py:

Found 4 contexts in gene subtable.
z1
z2
z3
z4

100%|██████████| 2064/2064 [00:01<00:00, 1746.92it/s]
Bivariate loglog regression results:
gamma = 0.6510109031387529
c = 0.2594626316691924
R2 = 0.8597118038702496

Gene: potF with R2=0.86
Data saved in kvalues_potF_Species_GTDB.tsv.
0%| | 0/2064 [00:00<?, ?it/s]
Traceback (most recent call last):

File "/Users/juanrivassantisteban/miniconda3/lib/python3.10/site-packages/spyder_kernels/py3compat.py", line 356, in compat_exec
exec(code, globals, locals)

File "/Users/juanrivassantisteban/Desktop/uGuilds-main/guild_tensors/guild_tensor_generate.py", line 129, in
gtutils.export_legacy(adu_table, _filepath, column="Diversity")

File "/Users/juanrivassantisteban/Desktop/uGuilds-main/guild_tensors/guild_tensor_utils.py", line 91, in export_legacy
assert sum(idx) == 1

AssertionError

Sometimes, the number of represented colors does not match with the actual legend colors.

When trying to run a master_tab with only GTDB taxonomic assigments, guild_tensor_generate.py is displaying this error:

   File "/Users/juanrivassantisteban/Desktop/uGuilds-main/guild_tensors/guild_tensor_utils.py", line 132, in check_mastertable
    idc_null = np.argwhere(df['Species_SQM'].isnull().values)[:, 0]

  File "/Users/juanrivassantisteban/miniconda3/lib/python3.10/site-packages/pandas/core/frame.py", line 3807, in __getitem__
    indexer = self.columns.get_loc(key)

  File "/Users/juanrivassantisteban/miniconda3/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3804, in get_loc
    raise KeyError(key) from err

KeyError: 'Species_SQM''

And if you add an empty column called "Species_SQM", the error changes to this one:

  File "/Users/juanrivassantisteban/Desktop/uGuilds-main/guild_tensors/guild_tensor_utils.py", line 144, in check_mastertable
    df.at[jj, "Genus_SQM"] = "GTDB:"+df.loc[jj, "Genus_GTDB"]

TypeError: can only concatenate str (not "float") to str

We need to compute diversity as the number of unique identifiers (rows) matching a value over 0 in the abundance column for any position in the k-tensor. Otherwise, diversity will always be the same (while abundance, of course, not) for every taxonomic level, regardless of the context.

guild_tensor_generate.py

If anyone wants to screen guilds in reduced contexts, this is, that not every single row the my master_tab.tsv will be classified in a context to visualize or to generate k-values, it would be useful to not getting this error in modify_mastertable.py:

ValueError: Length of values (2375) does not match length of index (91159)

It would be freaking good to compare distinct guild_tensors in the same plot.

Some concerns:

i) the k-values of different guilds can be in different magnitude orders. We should build a smart visualization!
ii) the resulting plot can represent an understanding-challenge. We should keep the things "easy".

It would be nice to add an argument for visualizing normalized abundances instead of k-values.

Because sometimes different clusters represent different genes, so regressions need to be gene- and context-specific.