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

Report glow up 2 [CW-7207]

Browse Source
This commit is contained in:
Neil Horner 2026-05-22 11:55:44 +00:00
parent 8c6196ddc1
commit f45056c438
2 changed files with 44 additions and 40 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

73
bin/workflow_glue/report.py
View File

@ -213,6 +213,27 @@ def _create_warning_banner(message, level="warning"):
raw(message)
def _volcano_style():
return raw("""
<style>
.volcano-table-grid {
display: grid;
grid-template-columns: repeat(2, minmax(0, 1fr));
gap: 20px 10px;
align-items: start;
}
.volcano-table-grid > * {
min-width: 0;
}
@media screen and (max-width: 1000px) {
.volcano-table-grid {
grid-template-columns: 1fr;
}
}
</style>
""")
def _as_string_list(value):
"""Normalize optional values to a compact list of strings."""
if value is None or value == "none":
@ -906,11 +927,7 @@ def main(args):
)
warnings_df = pd.DataFrame(warnings_data)
DataTable.from_pandas(
warnings_df,
paging=False,
use_index=False,
)
DataTable.from_pandas(warnings_df, paging=False, use_index=False)
with report.add_section("Differential gene expression", "DGE"):
tabs = Tabs()
@ -944,33 +961,15 @@ def main(args):
with p():
strong("Note: ")
raw(contrast_data["dtu_power_warning"])
DataTable.from_pandas(table, use_index=False)
h3("Gene expression volcano Plot")
vol, class_table, selected_table = volcano(table)
EZChart(vol, width="100%", height="550")
raw("""
<style>
.volcano-table-grid {
display: grid;
grid-template-columns: repeat(2, minmax(0, 1fr));
gap: 20px 10px;
align-items: start;
}
.volcano-table-grid > * {
min-width: 0;
}
@media screen and (max-width: 1000px) {
.volcano-table-grid {
grid-template-columns: 1fr;
}
}
</style>
""")
with div(_class="volcano-table-grid"):
EZChart(class_table, width="100%", height="auto")
EZChart(selected_table, width="100%", height="auto")
gn_vol, gn_class_table, gn_selected_table = volcano(table)
EZChart(gn_vol, width="100%", height="550")
with div(style=_volcano_style()):
with div(_class="volcano-table-grid"):
EZChart(gn_class_table, width="100%", height="auto")
EZChart(gn_selected_table, width="100%", height="auto")
with report.add_section("Differential transcript usage", "DTU"):
tabs = Tabs()
@ -1007,15 +1006,17 @@ def main(args):
level="warning",
)
# Show table if available
if contrast_name in dtu_tables:
DataTable.from_pandas(
dtu_tables[contrast_name],
use_index=False,
)
h3("Transcript expression volcano Plot")
# EZChart(volcano(dtu_tables[contrast_name]))
dtu_table = dtu_tables[contrast_name]
DataTable.from_pandas(dtu_table, use_index=False)
h3("Transcript expression volcano Plot")
tr_vol, tr_class_table, tr_selected_table = volcano(dtu_table)
EZChart(tr_vol, width="100%", height="550")
with div(style=_volcano_style()):
with div(_class="volcano-table-grid"):
EZChart(tr_class_table, width="100%", height="auto")
EZChart(tr_selected_table, width="100%", height="auto")
else:
p("No DTU results available for this contrast.")

11
bin/workflow_glue/volcano.py
View File

@ -768,8 +768,9 @@ def volcano(data, fold_threshold=1, p_threshold=0.05):
}
selected.forEach(function(index) {
if (view_toggle.active) {
selectedLabel[index] = \
data.gene_name[index] || data[identifier_col][index];
selectedLabel[index] = identifier_col === "TXNAME"
? data.TXNAME[index]
: (data.gene_name[index] || data[identifier_col][index]);
}
selectedData.source_index.push(index);
selectedData.owner_id.push(selected_source.id);
@ -900,8 +901,10 @@ def volcano(data, fold_threshold=1, p_threshold=0.05):
gene_name: [],
};
selection_state.data.indices[0].forEach(function(index) {
selectedLabel[index] = \
source.data.gene_name[index] || source.data[identifier_col][index];
selectedLabel[index] = identifier_col === "TXNAME"
? source.data.TXNAME[index]
: (source.data.gene_name[index] || \
source.data[identifier_col][index]);
highlightData.log2FoldChange.push(source.data.log2FoldChange[index]);
highlightData.neg_log10_padj.push(source.data.neg_log10_padj[index]);
highlightData.mean_expression.push(source.data.mean_expression[index]);