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Including number of samples in mutations in lineage plot #184

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merged 17 commits into from
Dec 20, 2024
Merged

Including number of samples in mutations in lineage plot #184

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1edb876
Introducing number of samples with selected lineage
Shettland Dec 20, 2024
ff4bbf4
Introducing number of samples with selected lineage.
Shettland Dec 20, 2024
4795816
Introducing n_samples var with num of samples
Shettland Dec 20, 2024
28537ee
Introducing n_samples var with num of samples
Shettland Dec 20, 2024
c247074
Introducing n_samples var with num of samples in app callback
Shettland Dec 20, 2024
8cd76e1
Introducing n_samples within dashbio needleplot
Shettland Dec 20, 2024
532cb04
Introducing n_samples within dashbio needleplot. fix
Shettland Dec 20, 2024
e7e64fd
Included num of samples inside mdata
Shettland Dec 20, 2024
811121c
Included num of samples inside mdata.
Shettland Dec 20, 2024
cc400f7
Including n_samples as new html div
Shettland Dec 20, 2024
02f1143
Including n_samples as new html div.
Shettland Dec 20, 2024
da4466b
Including n_samples div in app callback
Shettland Dec 20, 2024
69362ad
Including n_samples div in app callback fix
Shettland Dec 20, 2024
8a252be
Including n_samples div in app callback fix2
Shettland Dec 20, 2024
5c39d18
Including n_samples div in app callback fix3
Shettland Dec 20, 2024
2ac9cf7
Including n_samples div in app callback fix4
Shettland Dec 20, 2024
0719efa
Including n_samples div in app callback. linting
Shettland Dec 20, 2024
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38 changes: 23 additions & 15 deletions dashboard/utils/var_needle_mutation_graph_by_lineage.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,22 +29,20 @@ def get_variant_data_from_lineages(graphic_name=None, lineage=None, chromosome=N
# lineage_fieldID__property_name__iexact="lineage_name"
# ).exists():
# return None

all_lineages = core.models.LineageValues.objects.filter(
lineage_fieldID__property_name__iexact="lineage_name"
).values_list("value", flat=True)
if lineage is None:
lineage = (
core.models.LineageValues.objects.filter(
lineage_fieldID__property_name__iexact="lineage_name"
)
.values_list("value", flat=True)
.first()
)

lineage = all_lineages.first()
mdata = json_data[lineage]
n_samples = len([x for x in all_lineages if x == lineage])

return mdata, lineage
return mdata, lineage, n_samples


def create_needle_plot_graph_mutation_by_lineage(lineage_list, lineage, mdata):
def create_needle_plot_graph_mutation_by_lineage(
lineage_list, lineage, mdata, n_samples
):
options = []
for lin in lineage_list:
options.append({"label": lin, "value": lin})
Expand Down Expand Up @@ -80,10 +78,18 @@ def create_needle_plot_graph_mutation_by_lineage(lineage_list, lineage, mdata):
clearable=False,
multi=False,
value=lineage,
style={"width": "150px"},
style={"width": "150px", "margin-right": "30px"},
),
]
),
html.Div(
children=[
dcc.Markdown(
id="samples_markdown",
children=f"Showing mutations for {n_samples} samples",
)
]
),
],
style={
"display": "flex",
Expand All @@ -98,7 +104,7 @@ def create_needle_plot_graph_mutation_by_lineage(lineage_list, lineage, mdata):
mutationData=mdata,
rangeSlider=True,
xlabel="Genome Position",
ylabel="Population Allele Frequency ",
ylabel="Population Allele Frequency samples",
domainStyle={
# "textangle": "45",
"displayMinorDomains": False,
Expand All @@ -111,15 +117,17 @@ def create_needle_plot_graph_mutation_by_lineage(lineage_list, lineage, mdata):
@app.callback(
Output("dashbio-needleplot", "mutationData"),
Output("dashbio-needleplot", "lineage"),
Output("samples_markdown", "children"),
Input("needleplot-select-lineage", "value"),
)
def update_sample(selected_lineage):
mdata, lineage = get_variant_data_from_lineages(
mdata, lineage, n_samples = get_variant_data_from_lineages(
graphic_name="variations_per_lineage",
lineage=selected_lineage,
chromosome=None,
)
return mdata, lineage
markdown_text = f"Showing mutations for {n_samples} samples"
return mdata, lineage, markdown_text

@app.callback(
Output("dashbio-needleplot", "rangeSlider"),
Expand Down
4 changes: 2 additions & 2 deletions dashboard/views.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def mutations_in_lineage(request):
# mutations in lineages by lineage
def_chrom = core.utils.variants.get_default_chromosome()
lineages_list = core.utils.lineage.get_lineages_list()
mdata, lineage = (
mdata, lineage, n_samples = (
dashboard.utils.var_needle_mutation_graph_by_lineage.get_variant_data_from_lineages(
graphic_name="variations_per_lineage", lineage=None, chromosome=def_chrom
)
Expand All @@ -45,7 +45,7 @@ def mutations_in_lineage(request):
{"ERROR": dashboard.dashboard_config.ERROR_NO_LINEAGES_ARE_DEFINED_YET},
)
dashboard.utils.var_needle_mutation_graph_by_lineage.create_needle_plot_graph_mutation_by_lineage(
lineages_list, lineage, mdata
lineages_list, lineage, mdata, n_samples
)
return render(
request,
Expand Down
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