def _init_datatable_function(self, rois):
""" Initiate :class:`DataTableFunction` to create table to link each
row with sub HTML report. All table will have the same appearance. So,
let's initiate its only once.
"""
datatable_js = DataTableFunction(rois.df, 'roi')
datatable_js.datatable_options = {'scrollX': 'true',
'pageLength': 15,
'scrollCollapse' : 'true',
'dom': 'Bfrtip',
'buttons': ['copy', 'csv']}
return datatable_js
def test_datatables():
bed = bedtools.GenomeCov(sequana_data("JB409847.cov.csv"),
sequana_data("JB409847.gbk"))
rois = bed[0].get_roi()
rois.df['link'] = 'test'
datatable_js = DataTableFunction(rois.df, 'roi')
datatable_js.set_links_to_column('link', 'start')
datatable_js.datatable_options = {
'scrollX': 'true',
'pageLength': 15,
'scrollCollapse': 'true',
'dom': 'Bfrtip',
'buttons': ['copy', 'csv']
}
datatable = DataTable(rois.df, 'rois', datatable_js)
html_table = datatable.create_datatable(float_format='%.3g')
def init_roi_datatable(rois):
""" Initiate :class:`DataTableFunction` to create table to link each
row with sub HTML report. All table will have the same appearance.
We can therefore initialise the roi once for all.
:param rois: can be a ROIs from ChromosomeCov instance or a simple
dataframe
"""
# computed
try:
df = rois.df.copy()
except:
df = rois.copy()
df['link'] = ''
# set datatable options
datatable_js = DataTableFunction(df, 'roi')
if "start" in df.columns:
datatable_js.set_links_to_column('link', 'start')
if "end" in df.columns:
datatable_js.set_links_to_column('link', 'end')
datatable_js.datatable_options = {'scrollX': 'true',
'pageLength': 15,
'scrollCollapse' : 'true',
'dom': 'Bfrtip',
'buttons': ['copy', 'csv']}
return datatable_js
def test_datatables():
bed = bedtools.GenomeCov(sequana_data("JB409847.bed"),
sequana_data("JB409847.gbk"))
fasta = sequana_data("JB409847.fasta")
bed.compute_gc_content(fasta)
c = bed.chr_list[0]
c.run(4001)
rois = c.get_rois()
rois.df['link'] = 'test'
datatable_js = DataTableFunction(rois.df, 'roi')
datatable_js.set_links_to_column('link', 'start')
datatable_js.datatable_options = {'scrollX': 'true',
'pageLength': 15,
'scrollCollapse' : 'true',
'dom': 'Bfrtip',
'buttons': ['copy', 'csv']}
datatable = DataTable(rois.df, 'rois', datatable_js)
html_table = datatable.create_datatable(float_format='%.3g')
def test_datatables():
bed = bedtools.GenomeCov(sequana_data("JB409847.bed"),
sequana_data("JB409847.gbk"))
fasta = sequana_data("JB409847.fasta")
bed.compute_gc_content(fasta)
c = bed.chr_list[0]
c.run(4001)
rois = c.get_rois()
rois.df['link'] = 'test'
datatable_js = DataTableFunction(rois.df, 'roi')
datatable_js.set_links_to_column('link', 'start')
datatable_js.datatable_options = {
'scrollX': 'true',
'pageLength': 15,
'scrollCollapse': 'true',
'dom': 'Bfrtip',
'buttons': ['copy', 'csv']
}
datatable = DataTable(rois.df, 'rois', datatable_js)
html_table = datatable.create_datatable(float_format='%.3g')
def init_roi_datatable(chrom):
""" Initiate :class:`DataTableFunction` to create table to link each
row with sub HTML report. All table will have the same appearance. So,
let's initiate its only once.
"""
# get an roi df
df = chrom.get_roi().df.copy()
df['link'] = ''
# set datatable options
datatable_js = DataTableFunction(df, 'roi')
datatable_js.set_links_to_column('link', 'start')
datatable_js.set_links_to_column('link', 'end')
datatable_js.datatable_options = {
'scrollX': 'true',
'pageLength': 15,
'scrollCollapse': 'true',
'dom': 'Bfrtip',
'buttons': ['copy', 'csv']
}
return datatable_js