py2ls 0.2.4.6__py3-none-any.whl → 0.2.4.8__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- py2ls/.git/index +0 -0
- py2ls/batman.py +32 -1
- py2ls/bio.py +25 -22
- py2ls/data/usages_sns.json +2 -1
- py2ls/ips.py +1258 -724
- py2ls/ml2ls.py +1841 -390
- py2ls/plot.py +500 -235
- {py2ls-0.2.4.6.dist-info → py2ls-0.2.4.8.dist-info}/METADATA +2 -2
- {py2ls-0.2.4.6.dist-info → py2ls-0.2.4.8.dist-info}/RECORD +10 -10
- {py2ls-0.2.4.6.dist-info → py2ls-0.2.4.8.dist-info}/WHEEL +0 -0
py2ls/.git/index
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Binary file
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py2ls/batman.py
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@@ -37,7 +37,38 @@ def convert_to_html(text_list, strict=False):
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text = text.replace(escape_seq, html_rep)
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html_content += text.replace("\n", "<br>") # Add line breaks for newlines
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if strict:
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html_content = "<html><body>\n" + html_content + "\n</body></html>"
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# html_content = "<html><body>\n" + html_content + "\n</body></html>"
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# Include mobile-friendly CSS for responsive tables
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css_style = """
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<style>
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.table-container {
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overflow-x: auto;
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-webkit-overflow-scrolling: touch; /* Enable smooth scrolling on iOS */
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margin-bottom: 20px;
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}
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table {
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width: 100%;
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border-collapse: collapse;
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}
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th, td {
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padding: 8px;
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border: 1px solid #ddd;
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text-align: left;
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}
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</style>
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"""
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# Wrap the HTML content in the responsive container div
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html_content = f"""
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<html>
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<head>{css_style}</head>
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<body>
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<div class="table-container">
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{html_content}
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</div>
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</body>
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</html>
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"""
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return html_content
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py2ls/bio.py
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@@ -166,9 +166,23 @@ def get_probe(
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if platform_id is None:
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df_meta = get_meta(geo=geo, dataset=dataset, verbose=False)
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platform_id = df_meta["platform_id"].unique().tolist()
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platform_id = platform_id[0] if len(platform_id) == 1 else platform_id
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print(f"Platform: {platform_id}")
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if len(platform_id) > 1:
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df_probe= geo[dataset].gpls[platform_id[0]].table
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# df_probe=pd.DataFrame()
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# # Iterate over each platform ID and collect the probe tables
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# for platform_id_ in platform_id:
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# if platform_id_ in geo[dataset].gpls:
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# df_probe_ = geo[dataset].gpls[platform_id_].table
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# if not df_probe_.empty:
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# df_probe=pd.concat([df_probe, df_probe_])
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# else:
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# print(f"Warning: Probe table for platform {platform_id_} is empty.")
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# else:
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# print(f"Warning: Platform ID {platform_id_} not found in dataset {dataset}.")
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else:
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df_probe= geo[dataset].gpls[platform_id[0]].table
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if df_probe.empty:
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print(
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f"Warning: cannot find the probe info. 看一下是不是在单独的文件中包含了probe信息"
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@@ -215,9 +229,12 @@ def get_data(geo: dict, dataset: str = "GSE25097", verbose=False):
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df_expression = get_expression_data(geo, dataset=dataset)
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if not df_expression.select_dtypes(include=["number"]).empty:
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# 如果数据全部是counts类型的话, 则使用TMM进行normalize
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if 'counts' in get_data_type(df_expression):
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if 'counts' in get_data_type(df_expression):
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try:
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df_expression=counts2expression(df_expression.T).T
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print(f"{dataset}'s type is raw read counts, nomalized(transformed) via 'TMM'")
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except Exception as e:
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print("raw counts data")
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if any([df_probe.empty, df_expression.empty]):
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print(
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f"got empty values, check the probe info. 看一下是不是在单独的文件中包含了probe信息"
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@@ -237,23 +254,9 @@ def get_data(geo: dict, dataset: str = "GSE25097", verbose=False):
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# get meta info
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df_meta = get_meta(geo, dataset=dataset, verbose=False)
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col_rm = [
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"channel_count",
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"
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"
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"contact_city",
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"contact_country",
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"contact_department",
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"contact_email",
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"contact_institute",
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"contact_laboratory",
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"contact_name",
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"contact_phone",
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"contact_state",
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"contact_zip/postal_code",
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"contributor",
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"manufacture_protocol",
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"taxid",
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"web_link",
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"channel_count","contact_web_link","contact_address","contact_city","contact_country","contact_department",
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"contact_email","contact_institute","contact_laboratory","contact_name","contact_phone","contact_state",
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"contact_zip/postal_code","contributor","manufacture_protocol","taxid","web_link",
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]
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# rm unrelavent columns
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df_meta = df_meta.drop(columns=[col for col in col_rm if col in df_meta.columns])
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py2ls/data/usages_sns.json
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@@ -21,5 +21,6 @@
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"residplot": "seaborn.residplot(data=None,*,x=None,y=None,x_partial=None,y_partial=None,lowess=False,order=1,robust=False,dropna=True,label=None,color=None,scatter_kws=None,line_kws=None,ax=None)\nhttps://seaborn.pydata.org/generated/seaborn.residplot.html",
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"pairplot": "seaborn.pairplot(data,*,hue=None,hue_order=None,palette=None,vars=None,x_vars=None,y_vars=None,kind='scatter',diag_kind='auto',markers=None,height=2.5,aspect=1,corner=False,dropna=False,plot_kws=None,diag_kws=None,grid_kws=None,size=None)\nhttps://seaborn.pydata.org/generated/seaborn.pairplot.html",
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"jointplot": "seaborn.jointplot(data=None,*,x=None,y=None,hue=None,kind='scatter',height=6,ratio=5,space=0.2,dropna=False,xlim=None,ylim=None,color=None,palette=None,hue_order=None,hue_norm=None,marginal_ticks=False,joint_kws=None,marginal_kws=None,**kwargs)\nhttps://seaborn.pydata.org/generated/seaborn.jointplot.html",
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"plotting_context": "seaborn.plotting_context(context=None,font_scale=1,rc=None)\nhttps://seaborn.pydata.org/generated/seaborn.plotting_context.html"
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"plotting_context": "seaborn.plotting_context(context=None,font_scale=1,rc=None)\nhttps://seaborn.pydata.org/generated/seaborn.plotting_context.html",
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"swarmplot":"seaborn.swarmplot(data=None, *, x=None, y=None, hue=None, order=None, hue_order=None, dodge=False, orient=None, color=None, palette=None, size=5, edgecolor=None, linewidth=0, hue_norm=None, log_scale=None, native_scale=False, formatter=None, legend='auto', warn_thresh=0.05, ax=None, **kwargs)\nhttps://seaborn.pydata.org/generated/seaborn.swarmplot.html"
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}
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