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Python 50.44% Makefile 0.22% Jupyter Notebook 46.08% DM 0.63% Shell 0.25% R 2.38%

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jwdebelius nemochina2008 afcarl tkosciol kami-katze mbeck123

ggmap's Issues

rarefaction should preserve taxonomy if present

gray scale bars for low abundant taxa

create general caching function

executor: include timing as default

Emperor

add a function to create emperor plots for given beta div dict and metadata.

FutureWarning - corr_diversity

/tmp/ipykernel_2096454/2665748023.py:1: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.

sig_cols = {k for k,v in corr_diversity['results'].groupby('column')['p-value'].min().iteritems()

include calour in requirements

unittest drawMap

currently, there is no unittest for drawMap in place, also the docstring is quite ugly.

user defined path for temporary directory

The function "_executor" in the script "analysis.py" at the path "ggmap/ggmap/analysis.py" should provide a new parameter to set a user defined path for "dir_temp" when using "use_grid".

check if sepp need "environment"

Add reference to switch to Challenge 1 before doing step 8

cache: auto remove

automatically remove cache file if size == 0b because this is due to a faulty run

rarefaction curves in QIIME cause some problems + are ugly, i.e. re-scaling is not possible. I also don't understand why it is necessary to look at several metadata columns.
Therefore, I should go with plt.plot() and do the single plots by myself.
Also: caching is possible when storing grouped values instead of IMAGES.

timing & SEPP

Why is stderr and stdout in wrong places ./ instead of TMP/ ?

executor: check crawldir by default

add picrust to analyses

make taxplot part of plot() not a separate figure

unit tests for all three functions for find_diff_taxa

cover snippets functions with unittests

Challenge 2: insert ppn=1

space between every bar

hide sample numbers

FutureWarning - plotTaxonomy

/homes/tbaeuerl/ggmap/ggmap/snippets.py:449: FutureWarning: The default value of numeric_only in DataFrameGroupBy.sum is deprecated. In a future version, numeric_only will default to False. Either specify numeric_only or select only columns which should be valid for the function.

counts_taxonomy = counts_taxonomy.reset_index().groupby(rank).sum()

/homes/tbaeuerl/ggmap/ggmap/snippets.py:702: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.

rank_counts = rank_counts.append(lowReadTaxa)

activate new conda environment: conda activate ggmap
clone github repo via: git clone https://github.com/sjanssen2/ggmap.git
cd into the new directory cd ggmap
install modules from sources python setup.py develop --user

to:

activate new conda environment: conda activate ggmap
clone github repo via: git clone https://github.com/sjanssen2/ggmap.git
cd into the new directory cd ggmap
install Python for conda env: conda install python
install modules from sources: python setup.py develop