KeyError: at plot_group_stats step about scdrs

[KangchengHou]

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:

1. 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

scDRS/scdrs/util.py

Line 451 in 06e6df0

def plot_group_stats(

2. 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)

[vicscott]

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.

[KangchengHou]

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?

[vicscott]

My scrds version is v1.0.1, and it still report like above after I run these git and pip commands. By the way, thanks for your reply.

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---Original--- From: "Kangcheng ***@***.***> Date: Fri, Sep 9, 2022 23:48 PM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [martinjzhang/scDRS] KeyError: at plot_group_stats step (Issue #24) 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? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KangchengHou]

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?

[vicscott]

I found that the function called group_stats containing the argument "fdr_prop" was deprecated in method.py, but "fdr_prop" was still a requisite for the function called plot_group_stats.

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---Original--- From: "Kangcheng ***@***.***> Date: Sat, Sep 10, 2022 00:08 AM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [martinjzhang/scDRS] KeyError: at plot_group_stats step (Issue#24) 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? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KangchengHou]

Hi please try pip install scdrs==1.0.2 and feel free to reopen if this bug pertains.

[econnolly7]

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!

[martinjzhang]

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

[KangchengHou]

@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)

[vicscott]

I am sure that the version is v1.0.1, vic ***@***.***  

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------------------ 原始邮件 ------------------ 发件人: "martinjzhang/scDRS" ***@***.***>; 发送时间: 2022年9月10日(星期六) 凌晨0:08 ***@***.***>; ***@***.******@***.***>; 主题: Re: [martinjzhang/scDRS] KeyError: at plot_group_stats step (Issue #24) 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? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[KangchengHou]

this should be addressed in f1b83e4. feel free to reopen