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Add color scheme selection and intersection/union method for visualiz…
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…ations.
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@PaulArthurM
PaulArthurM committed Feb 10, 2022
1 parent cd5c37e commit 3d4de7f
Showing 1 changed file with 60 additions and 20 deletions.
80 changes: 60 additions & 20 deletions PitViper/workflow/notebooks/functions_pitviper_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -749,11 +749,17 @@ def show_sgRNA_counts(token):
cts_columns = [col for col in cts.columns.tolist() if not col in ["sgRNA", "Gene"]]
cts = pd.melt(cts, id_vars=['sgRNA', 'Gene'])
genes_list = list(set(cts.Gene.tolist()))

color_schemes = ["blueorange", "brownbluegreen", "purplegreen", "pinkyellowgreen", "purpleorange", "redblue", "redgrey", "redyellowblue", "redyellowgreen", "spectral"]

element = widgets.Combobox(placeholder='Choose one', options = genes_list, description='Element:', value=genes_list[0], ensure_option=False)
conditions = widgets.TagsInput(value=cts_columns, allowed_tags=cts_columns, allow_duplicates=False)
color_scheme_widget = widgets.Dropdown(placeholder='Choose one', options = color_schemes, description='Color scheme:', value=color_schemes[0])
reverse_widget = widgets.Checkbox(value=False, description='Reverse color scheme?')

display(element)
display(conditions)
# display(element)
# display(conditions)
display(widgets.VBox([element, conditions, color_scheme_widget, reverse_widget]))

button = widgets.Button(description="Show!")
display(button)
Expand All @@ -780,7 +786,7 @@ def on_button_clicked(b):
).mark_rect().encode(
x=alt.X('variable', axis=alt.Axis(title='Replicate'), sort=conditions.value),
y=alt.Y('sgRNA', axis=alt.Axis(title='sgRNA')),
color=alt.Color('z-score:Q',scale=alt.Scale(scheme='blueorange')),
color=alt.Color('z-score:Q',scale=alt.Scale(scheme=color_scheme_widget.value, reverse=reverse_widget.value)),
tooltip=['sgRNA', 'variable', 'value', 'z-score']
).interactive()
display(chart)
Expand Down Expand Up @@ -1715,6 +1721,14 @@ def GSEA_like_score_update(change):
GSEA_like_fdr.observe(GSEA_like_fdr_update, 'value')


def disable_widgets(token):
config = "./config/%s.yaml" % token
content = open_yaml(config)
disabled = False
if content['screen_type'] == 'not_gene':
disabled = True
return disabled


def multiple_tools_results(tools_available, token):
TOOLS = [tool for tool in tools_available.keys() if not tool in ["DESeq2"]]
Expand All @@ -1726,6 +1740,7 @@ def multiple_tools_results(tools_available, token):
# Define widgets
conditions_widget = widgets.Dropdown(options=conditions_options, description = "Conditions:")
tools_widget = widgets.SelectMultiple(options=tools_options, description = "Tool:")
selection_widgets = widgets.ToggleButtons(options=['Intersection', 'Union'], description='Selection mode:', tooltips=['Use elements at intersection of all selected methods', 'Use union of elements of all selected methods'])

output_tools_form = widgets.Output()

Expand All @@ -1738,61 +1753,81 @@ def tools_widget_updated(event):
display_tools_widgets(event['new'])

tools_widget.observe(tools_widget_updated, 'value')
display(widgets.VBox([conditions_widget, tools_widget]))
display(widgets.VBox([conditions_widget, tools_widget, selection_widgets]))
display(output_tools_form)

disabled = disable_widgets(token)
venn_button = widgets.Button(description="Venn diagram", style=dict(button_color='#707070'))
rra_button = widgets.Button(description="RRA ranking", style=dict(button_color='#707070'))
genemania_button = widgets.Button(description="Genemania", style=dict(button_color='#707070'))
enrichr_button = widgets.Button(description="EnrichR", style=dict(button_color='#707070'))
depmap_button = widgets.Button(description="depmap", style=dict(button_color='#707070'))

ranking_button = widgets.Button(description="ranking", style=dict(button_color='#707070'))
genemania_button = widgets.Button(description="Genemania", style=dict(button_color='#707070'), disabled=disabled)
enrichr_button = widgets.Button(description="EnrichR", style=dict(button_color='#707070'), disabled=disabled)
depmap_button = widgets.Button(description="depmap", style=dict(button_color='#707070'), disabled=disabled)
ranking_button = widgets.Button(description="Save ranking", style=dict(button_color='#707070'))

buttons_box = widgets.HBox([venn_button, rra_button, genemania_button, enrichr_button, depmap_button, ranking_button])
display(buttons_box)

def venn_button_clicked(b):
treatment, control = conditions_widget.value.split("_vs_")
ranks, occurences = ranking(treatment, control, token, tools_available, params)
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).all(1), columns = ['intersection'])
intersection_genes = df.loc[df.intersection == True].index
if selection_widgets.value == "Intersection":
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).all(1), columns = ['intersection'])
genes_list = df.loc[df.intersection == True].index
else:
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).any(1), columns = ['union'])
genes_list = df.loc[df.union == True].index
plot_venn(occurences)
print("Genes at intersection of all methods:")
for gene in intersection_genes:
print("Genes at %s of all methods:" % selection_widgets.value)
for gene in genes_list:
print(gene)

def rra_button_clicked(b):
treatment, control = conditions_widget.value.split("_vs_")
ranks, occurences = ranking(treatment, control, token, tools_available, params)
print("\n\n########################################")
print("### RRA results ###")
run_rra(ranks)
print("########################################")

def genemania_button_clicked(b):
treatment, control = conditions_widget.value.split("_vs_")
ranks, occurences = ranking(treatment, control, token, tools_available, params)
genes_list = list(occurences[occurences.all(axis='columns')].index)
print("\n\n########################################")
print("### Genemania link using %s" % selection_widgets.value)
if selection_widgets.value == "Intersection":
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).all(1), columns = ['intersection'])
genes_list = df.loc[df.intersection == True].index
else:
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).any(1), columns = ['union'])
genes_list = df.loc[df.union == True].index
link = "http://genemania.org/search/homo-sapiens/" + "/".join(genes_list)
print('Link to Genemania website: (%s elements)\n' % len(genes_list))
print(link)
print("########################################")

def enrichr_button_clicked(b):
def test(b, genes, bases, size, plot_type, col_2, col_1, description):
def show_enrichr_plots(b, genes, bases, size, plot_type, col_2, col_1, description):
charts = []
title = description.value + " (%s)" % selection_widgets.value
for base in bases.value:
enrichr_res = getEnrichrResults(genes, description.value, base)
table = createEnrichrTable(enrichr_res)
if plot_type.value == 'Bar':
chart = enrichmentBarPlot(table, size.value, description.value, col_1.value, col_2.value, base)
chart = enrichmentBarPlot(table, size.value, title, col_1.value, col_2.value, base)
else:
chart = enrichmentCirclePlot(table, size.value, description.value, col_1.value, col_2.value, base)
chart = enrichmentCirclePlot(table, size.value, title, col_1.value, col_2.value, base)
charts.append(chart)
for chart in charts:
display(chart)

treatment, control = conditions_widget.value.split("_vs_")
ranks, occurences = ranking(treatment, control, token, tools_available, params)
genes_list = list(occurences[occurences.all(axis='columns')].index)
if selection_widgets.value == "Intersection":
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).all(1), columns = ['intersection'])
genes_list = df.loc[df.intersection == True].index
else:
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).any(1), columns = ['union'])
genes_list = df.loc[df.union == True].index
BASES = open("workflow/notebooks/enrichr_list.txt", "r").readlines()
bases = widgets.SelectMultiple(options=BASES, description="Gene sets:", rows=10)
col_2 = widgets.ColorPicker(concise=False, description='Top color', value='blue')
Expand All @@ -1803,7 +1838,7 @@ def test(b, genes, bases, size, plot_type, col_2, col_1, description):
button_enrichr = widgets.Button(description="EnrichR!")

display(widgets.VBox([description, bases, plot_type, size, col_2, col_1, button_enrichr]))
button_enrichr.on_click(partial(test, genes=genes_list, bases=bases, size=size, plot_type=plot_type, col_2=col_2, col_1=col_1, description=description))
button_enrichr.on_click(partial(show_enrichr_plots, genes=genes_list, bases=bases, size=size, plot_type=plot_type, col_2=col_2, col_1=col_1, description=description))


def depmap_button_clicked(b):
Expand Down Expand Up @@ -1930,7 +1965,12 @@ def tissu_selection_button_clicked(b):
cell_lines_selected = cell_lines_widget.value
boolean_series = table.cell_line_name.isin(cell_lines_selected)
table = table[boolean_series]
genes_list = list(occurences[occurences.all(axis='columns')].index)
if selection_widgets.value == "Intersection":
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).all(1), columns = ['intersection'])
genes_list = df.loc[df.intersection == True].index
else:
df = pd.DataFrame(occurences.eq(occurences.iloc[:, 0], axis=0).any(1), columns = ['union'])
genes_list = df.loc[df.union == True].index
if data_types_widget.value == "mutations":
columns = ['gene_name', 'cell_line', 'cell_line_name', 'sample_collection_site', 'primary_or_metastasis', 'primary_disease','subtype_disease']
for value in variable:
Expand Down

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