-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
248 additions
and
248 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,90 +1,90 @@ | ||
| from shiny import App, reactive, ui, render, Session | ||
| import scanpy as sc | ||
| import os | ||
| import tempfile | ||
| import anndata as ad | ||
| import pandas as pd | ||
|
|
||
| from sliders import slider_ui, slider_server | ||
| from distributions import distributions_server | ||
| from plots import plots_server, plots_ui | ||
| from metadata import metadata_server, metadata_ui | ||
| from helpers import calculate_qc_metrics | ||
|
|
||
|
|
||
| _pretty_names = reactive.value({ | ||
| 'total_counts': 'Total counts', | ||
| 'n_genes_by_counts': 'Number of genes with counts', | ||
| 'pct_counts_mt': 'Percentage of counts from mitochondrial genes', | ||
| }) | ||
|
|
||
|
|
||
| app_ui = ui.page_navbar( | ||
| ui.nav_panel("1. Upload", ui.input_file("file_input", label="Upload your file", accept=".h5ad")), | ||
| ui.nav_panel("2. Metadata", metadata_ui("metadata")), | ||
| ui.nav_panel("3. Quality control", | ||
| ui.layout_sidebar( | ||
| ui.sidebar( | ||
| slider_ui("sliders") | ||
| ), | ||
| plots_ui("plots") | ||
| ) | ||
| ), | ||
| ui.nav_panel("4. Download", | ||
| ui.download_button("download", "Download filtered data") | ||
| ), | ||
| title="Preprocessing for SIMBA🦁", | ||
| window_title="SIMBA🦁: Preprocessing" | ||
| ) | ||
|
|
||
|
|
||
| def server(input, output, session: Session): | ||
| _adata: reactive.Value[ad.AnnData] = reactive.value(None) | ||
| _adata_meta: reactive.Value[ad.AnnData] = reactive.value(None) | ||
| _adata_filtered: reactive.Value[ad.AnnData] = reactive.value(None) | ||
| _file_name = reactive.value(None) | ||
| _distributions = reactive.value({}) | ||
| _metadata = reactive.value(None) | ||
| _calculate_metrics_bool = reactive.value(False) | ||
|
|
||
| distributions_server("distributions", _adata_meta, _pretty_names, _distributions) | ||
| slider_server("sliders", _adata, _metadata, _adata_meta, _adata_filtered, _pretty_names, _distributions, _calculate_metrics_bool) | ||
| plots_server("plots", _adata_filtered, _pretty_names, _distributions) | ||
| metadata_server("metadata", _adata, _metadata) | ||
|
|
||
| @reactive.effect | ||
| def load_adata(): | ||
| file = input["file_input"].get() | ||
| if file is None: | ||
| return | ||
| if len(file) > 1: | ||
| print("Only one file at a time") | ||
| return | ||
|
|
||
| used_file = file[0] | ||
| _file_name.set(used_file["name"]) | ||
| adata = sc.read_h5ad(used_file["datapath"]) | ||
| _adata.set(adata) | ||
| _calculate_metrics_bool.set(True) | ||
|
|
||
| @reactive.effect | ||
| def update_adata_meta(): | ||
| adata = _adata.get() | ||
| metadata = _metadata.get() | ||
| if adata is None or metadata is None: | ||
| return | ||
| _calculate_metrics_bool.set(True) | ||
|
|
||
| @render.download( | ||
| filename = lambda: _file_name.get().replace(".h5ad", "_filtered.h5ad"), | ||
| ) | ||
| def download(): | ||
| adata_filtered = _adata_filtered.get() | ||
| if adata_filtered is None: | ||
| return | ||
|
|
||
| with tempfile.NamedTemporaryFile(suffix=".h5ad", delete=False) as temp: | ||
| adata_filtered.write(temp.name) | ||
| return temp.name | ||
|
|
||
| app = App(app_ui, server, static_assets=os.path.join(os.path.dirname(__file__), "media")) | ||
| from shiny import App, reactive, ui, render, Session | ||
| import scanpy as sc | ||
| import os | ||
| import tempfile | ||
| import anndata as ad | ||
| import pandas as pd | ||
|
|
||
| from sliders import slider_ui, slider_server | ||
| from distributions import distributions_server | ||
| from plots import plots_server, plots_ui | ||
| from metadata import metadata_server, metadata_ui | ||
| from helpers import calculate_qc_metrics | ||
|
|
||
|
|
||
| _pretty_names = reactive.value({ | ||
| 'total_counts': 'Total counts', | ||
| 'n_genes_by_counts': 'Number of genes with counts', | ||
| 'pct_counts_mt': 'Percentage of counts from mitochondrial genes', | ||
| }) | ||
|
|
||
|
|
||
| app_ui = ui.page_navbar( | ||
| ui.nav_panel("1. Upload", ui.input_file("file_input", label="Upload your file", accept=".h5ad")), | ||
| ui.nav_panel("2. Metadata", metadata_ui("metadata")), | ||
| ui.nav_panel("3. Quality control", | ||
| ui.layout_sidebar( | ||
| ui.sidebar( | ||
| slider_ui("sliders") | ||
| ), | ||
| plots_ui("plots") | ||
| ) | ||
| ), | ||
| ui.nav_panel("4. Download", | ||
| ui.download_button("download", "Download filtered data") | ||
| ), | ||
| title="Preprocessing for SIMBA🦁", | ||
| window_title="SIMBA🦁: Preprocessing" | ||
| ) | ||
|
|
||
|
|
||
| def server(input, output, session: Session): | ||
| _adata: reactive.Value[ad.AnnData] = reactive.value(None) | ||
| _adata_meta: reactive.Value[ad.AnnData] = reactive.value(None) | ||
| _adata_filtered: reactive.Value[ad.AnnData] = reactive.value(None) | ||
| _file_name = reactive.value(None) | ||
| _distributions = reactive.value({}) | ||
| _metadata = reactive.value(None) | ||
| _calculate_metrics_bool = reactive.value(False) | ||
|
|
||
| distributions_server("distributions", _adata_meta, _pretty_names, _distributions) | ||
| slider_server("sliders", _adata, _metadata, _adata_meta, _adata_filtered, _pretty_names, _distributions, _calculate_metrics_bool) | ||
| plots_server("plots", _adata_filtered, _pretty_names, _distributions) | ||
| metadata_server("metadata", _adata, _metadata) | ||
|
|
||
| @reactive.effect | ||
| def load_adata(): | ||
| file = input["file_input"].get() | ||
| if file is None: | ||
| return | ||
| if len(file) > 1: | ||
| print("Only one file at a time") | ||
| return | ||
|
|
||
| used_file = file[0] | ||
| _file_name.set(used_file["name"]) | ||
| adata = sc.read_h5ad(used_file["datapath"]) | ||
| _adata.set(adata) | ||
| _calculate_metrics_bool.set(True) | ||
|
|
||
| @reactive.effect | ||
| def update_adata_meta(): | ||
| adata = _adata.get() | ||
| metadata = _metadata.get() | ||
| if adata is None or metadata is None: | ||
| return | ||
| _calculate_metrics_bool.set(True) | ||
|
|
||
| @render.download( | ||
| filename = lambda: _file_name.get().replace(".h5ad", "_filtered.h5ad"), | ||
| ) | ||
| def download(): | ||
| adata_filtered = _adata_filtered.get() | ||
| if adata_filtered is None: | ||
| return | ||
|
|
||
| with tempfile.NamedTemporaryFile(suffix=".h5ad", delete=False) as temp: | ||
| adata_filtered.write(temp.name) | ||
| return temp.name | ||
|
|
||
| app = App(app_ui, server, static_assets=os.path.join(os.path.dirname(__file__), "media")) |
Oops, something went wrong.