Comments (12)
This should be due to some version inconsistency (we updated scdrs.util.plot_group_stats
only very recently, sorry!)
Follows are options you can proceed:
- update to the github master version:
git clone https://github.com/martinjzhang/scDRS.git
cd scDRS
pip install -e .
which will use the latest code
Line 451 in 06e6df0
- skip the plotting for now until we push another release (you should be able to run through other parts of the tutorial without calling this function)
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I met the same problem. So I would like to appreciate if there are some advice to plot like scdrs.util.plot_group_stats
according to the scdrs_group.level1class file. And another question is that I don't known what happened to my scdrs_group.level1class file that the nfdr_* are all 0.
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hi @vicscott can you try
git clone https://github.com/martinjzhang/scDRS.git
cd scDRS
pip install -e .
to update to the latest version (we will soon push that to the pip). And can you replicate what you are seeing following https://martinjzhang.github.io/scDRS/notebooks/quickstart.html?
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that bug is fixed after v1.0.1 (and we will have a new version for that). For scdrs_group.level1class
Could you confirm you are seeing different things than this?
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Hi please try pip install scdrs==1.0.2
and feel free to reopen if this bug pertains.
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Hi there. Awesome package. I just installed scdrs v1.0.2 and after running plot_group_stats() on the demo dataset from the quickstart guide I get the following error:
util.py:557: UserWarning: Tight layout not applied. The bottom and top margins cannot be made large enough to accommodate all axes decorations.
Let me know what I should do. Thanks so much!
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Hi,
This seems to be due to the figure size being too small. Having a larger figure should fix the problem, e.g., plt.figure(figsize=[width, height])
with large numbers for width
and height
.
I will wait for @KangchengHou for more detailed replies.
Best,
Martin
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@econnolly7 yes it is due to plotting settings. I will add more options to the plotting functions and will reply further here.
But you should be able to proceed the rest of the tutorial (e.g., looking at the numerical results)
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this should be addressed in f1b83e4. feel free to reopen
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Related Issues (20)
- custom gene set ? HOT 2
- The graphs from a single result and multiple results are inconsistent HOT 13
- Subsetting cells for downstream analysis. HOT 1
- TypeError: '<' not supported between instances of 'str' and 'float' HOT 3
- About compute-score
- Is it reasonable to use human' geneset on mouse scRNAseq data? HOT 2
- TypeError: plot_group_stats() got an unexpected keyword argument 'plot_kws' HOT 16
- trait=z_score: skipped due to small size (n_gene=5, sys_time=116.1s) HOT 1
- AssertionError when running quick test after installation HOT 7
- The 'n_fdr_0.2' number of all group is 0 HOT 7
- Interpreting scDRS score when comparing cell-type subclusters HOT 1
- Using geneset from SMR result HOT 1
- ValueError: too many values to unpack (expected 2) HOT 8
- Converting GWAS catalog .tsv file to gene set HOT 3
- Preprocessing: killed running scdrs compute-score HOT 4
- tcell.facs.annot.h5ad without GENE name HOT 2
- use scdrs in a tissue seemlingly unrelated with the disease HOT 4
- fail to get the "1000 top associated genes" based on MAGMA HOT 2
- Correcting cell-level p-values for multiple comparisons? HOT 3
- Questions about matched gene sets HOT 2
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