kfukuta/wf-transcriptomes-v202
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Condition report fix [CW-7283]

Browse Source
This commit is contained in:
Neil Horner 2026-05-27 15:05:18 +00:00
parent 10b2013b6a
commit 3e53b755cc
1 changed files with 18 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

24
bin/workflow_glue/hierarchical_clustering.py
View File

@ -177,14 +177,14 @@ def _add_colour(samples, condition_column):
return samples
def _condition_strip_plot(sample_metadata, col_order, x_range):
def _condition_strip_plot(sample_metadata, col_order, x_range, condition_column):
"""Build a compact condition strip aligned to the heatmap columns."""
smeta = sample_metadata.iloc[col_order]
condition_height = int(TOP_DENDROGRAM_HEIGHT * 0.5)
strip_source = ColumnDataSource({
"x": np.arange(len(smeta)),
"sample": smeta["sample"].tolist(),
"condition": smeta["condition"].tolist(),
"condition": smeta[condition_column].tolist(),
"sample_color": smeta["contrast_color"].tolist(),
})
strip = figure(
@ -355,8 +355,15 @@ def distance_plot(matrix, col_order, sample_names, height):
def heatmap_plot(
z_matrix, labels, sample_names, row_linkage, col_linkage, sample_metadata, col_order
):
z_matrix,
labels,
sample_names,
row_linkage,
col_linkage,
sample_metadata,
col_order,
condition_column,
):
"""Build the clustered heatmap and row dendrogram layout."""
n_rows, n_cols = z_matrix.shape
x_values = np.tile(np.arange(n_cols), n_rows)
@ -456,7 +463,9 @@ def heatmap_plot(
final_fig = BokehPlot()
if sample_metadata is not None:
strip_height = int(TOP_DENDROGRAM_HEIGHT * 0.5)
strip = _condition_strip_plot(sample_metadata, col_order, heatmap.x_range)
strip = _condition_strip_plot(
sample_metadata, col_order, heatmap.x_range, condition_column
)
left_column = bokeh_column(
sample_dendro_fig, strip, heatmap, sizing_mode="stretch_width", spacing=0)
right_column = bokeh_column(
@ -482,6 +491,8 @@ def pca_plot(matrix, col_order, sample_names, sample_metadata, condition_column)
pca_data = _sample_pca(matrix[:, col_order], sample_names)
if sample_metadata is not None:
pca_data = pca_data.merge(sample_metadata, on="sample", how="left")
if condition_column in pca_data.columns:
pca_data["condition"] = pca_data[condition_column]
else:
pca_data["contrast_color"] = "#4C78A8"
@ -590,7 +601,8 @@ def hierarchical(
row_linkage=row_linkage,
col_linkage=col_linkage,
sample_metadata=meta,
col_order=col_order
col_order=col_order,
condition_column=condition_column,
)
pca_plt = pca_plot(
matrix=log2_matrix,