kb_python.report¶
Module Contents¶
Functions¶
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Convert a dictionary to a Plot.ly table of key-value pairs. |
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Generate knee plot card. |
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Generate genes detected plot card. |
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Generate elbow plot card. |
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Generate PCA plot card. |
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Render the Jupyter notebook report with Jinja2. |
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Execute the report and write the results as a Jupyter notebook and HTML. |
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Render and execute the report. |
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kb_python.report.logger¶
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kb_python.report.REPORT_DIR¶
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kb_python.report.BASIC_TEMPLATE_PATH¶
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kb_python.report.MATRIX_TEMPLATE_PATH¶
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kb_python.report.MARGIN¶
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kb_python.report.dict_to_table(d, column_ratio=[3, 7], column_align=['right', 'left'])¶ Convert a dictionary to a Plot.ly table of key-value pairs.
- Parameters
d (dict) – dictionary to convert
column_ratio (list, optional) – relative column widths, represented as a ratio, defaults to [3, 7]
column_align (list, optional) – column text alignments, defaults to [‘right’, ‘left’]
- Returns
figure
- Return type
plotly.graph_objs.Figure
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kb_python.report.knee_plot(n_counts)¶ Generate knee plot card.
- Parameters
n_counts (list) – list of UMI counts
- Returns
figure
- Return type
plotly.graph_objs.Figure
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kb_python.report.genes_detected_plot(n_counts, n_genes)¶ Generate genes detected plot card.
- Parameters
n_counts (list) – list of UMI counts
n_genes (list) – list of gene counts
- Returns
figure
- Return type
plotly.graph_objs.Figure
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kb_python.report.elbow_plot(pca_variance_ratio)¶ Generate elbow plot card.
- Parameters
pca_variance_ratio (list) – list PCA variance ratios
- Returns
figure
- Return type
plotly.graph_objs.Figure
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kb_python.report.pca_plot(pc)¶ Generate PCA plot card.
- Parameters
pc (list) – embeddings
- Returns
figure
- Return type
plotly.graph_objs.Figure
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kb_python.report.write_report(stats_path, info_path, inspect_path, out_path, matrix_path=None, barcodes_path=None, genes_path=None, t2g_path=None)¶ Render the Jupyter notebook report with Jinja2.
- Parameters
stats_path (str) – path to kb stats JSON
info_path (str) – path to run_info.json
inspect_path (str) – path to inspect.json
out_path (str) – path to Jupyter notebook to generate
matrix_path (str) – path to matrix
barcodes_path (str) – list of paths to barcodes.txt
genes_path (str, optional) – path to genes.txt, defaults to None
t2g_path (str) – path to transcript-to-gene mapping
- Returns
path to notebook generated
- Return type
str
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kb_python.report.execute_report(execute_path, nb_path, html_path)¶ Execute the report and write the results as a Jupyter notebook and HTML.
- Parameters
execute_path (str) – path to Jupyter notebook to execute
nb_path (str) – path to Jupyter notebook to generate
html_path (str) – path to HTML to generate
- Returns
tuple containing executed notebook and HTML
- Return type
tuple
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kb_python.report.render_report(stats_path, info_path, inspect_path, nb_path, html_path, matrix_path=None, barcodes_path=None, genes_path=None, t2g_path=None, temp_dir='tmp')¶ Render and execute the report.
- Parameters
stats_path (str) – path to kb stats JSON
info_path (str) – path to run_info.json
inspect_path (str) – path to inspect.json
nb_path (str) – path to Jupyter notebook to generate
html_path (str) – path to HTML to generate
matrix_path (str) – path to matrix
barcodes_path (str) – list of paths to barcodes.txt
genes_path (str, optional) – path to genes.txt, defaults to None
t2g_path (str) – path to transcript-to-gene mapping
temp_dir (str, optional) – path to temporary directory, defaults to tmp
- Returns
dictionary containing notebook and HTML paths
- Return type
dict