def boxplot(self, target="", width=300, height=300, data=None):
if not target:
target = 'div_boxplot_'+ipyTools.random_str()
html = "<div id='%s'></div>"%(target)
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
if data is None:
data = "Retina.RendererInstances.boxplot[0].exampleData()"
else:
data = json.dumps(data)
opt = "target: document.getElementById('%s'), width: %d, height: %d, data: %s"%(target, width, height, data)
src = """
(function(){
Retina.load_renderer('boxplot').then( function () { Retina.Renderer.create('boxplot', {""" + opt + """} ).render(); } );
})();
"""
if self.debug:
print src
else:
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
def paragraph(self, width='940', target="", data=None, title_color='black', header_color='black', text_color='black', raw=False):
if not target:
target = 'div_para_'+ipyTools.random_str()
html = "<div id='%s'></div>"%(target)
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
if data is None:
data = "Retina.RendererInstances.paragraph[0].exampleData()"
else:
data = json.dumps(data)
opt = "width: '%s', target: document.getElementById('%s'), data: %s, title_color: '%s', header_color: '%s', text_color: '%s', raw: %s"%(width, target, data, title_color, header_color, text_color, self._bool(raw))
src = """
(function(){
Retina.load_renderer('paragraph').then( function () { Retina.Renderer.create('paragraph', {""" + opt + """} ).render(); } );
})();
"""
if self.debug:
print src
else:
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
def heatmap(self, width=700, height=600, target="", data=None, tree_height=50, tree_width=50, legend_height=250, legend_width=250, row_text_size=15, col_text_size=15, min_cell_height=19, selectedRows=[], onclick=None):
"""Heatmap Renderer
Displays a heatmap.
Options
width (int)
Number of pixels the resulting image is wide. Default is 700
height (int)
Number of pixels the resulting image is high. This will be adjusted to at least rows * min_cell_height + legend and tree heights. Default is 600.
tree_height (int)
Number of pixels the dendogram tree for the columns is high. Default is 50.
tree_width (int)
Number of pixels the dendogram tree for the rows is wide. Default is 50.
legend_height (int)
Number of pixels for the column names. Default is 250.
legend_width (int)
Number of pixels for the row names. Default is 250.
row_text_size (int)
Number of pixels of the row text font size. Default is 15.
col_text_size (int)
Number of pixels of the column text font size. Default is 15.
min_cell_height (int)
Minimum number of pixels a row is high. This may cause the defined height of the resulting image to be overwritten. Default is 19.
selectedRows (array of boolean)
Returns an array that has a value of true for all row indices that are currently selected.
data (object)
columns (array of string)
names of the columns
rows (array of string)
names of the rows
colindex (array of int)
1 based indices of the original column order. This converts the original order (columns) into the one ordered by distance.
rowindex (array of int)
1 based indices of the original row order. This converts the original order (rows) into the one ordered by distance.
coldend (array of array of float)
distance matrix for the columns
rowdend
distance matrix for the rows
data (array of array of float)
normalized value matrix
"""
if not target:
target = 'div_heatmap_'+ipyTools.random_str()
html = "<div id='%s'></div>"%(target)
rows = '[""]'
if data is None:
data = "Retina.RendererInstances.heatmap[0].exampleData()"
else:
rows = json.dumps(data['rows'])
data = json.dumps(data)
selectedRows = json.dumps(selectedRows)
hname = 'heatmap_'+ipyTools.random_str()
opt = "width: %d, height: %d, target: document.getElementById('%s'), data: %s, selectedRows: %s, tree_height: %d, tree_width: %d, legend_height: %d, legend_width: %d, row_text_size: %d, col_text_size: %d, min_cell_height: %d"%(width, height, target, data, selectedRows, tree_height, tree_width, legend_height, legend_width, row_text_size, col_text_size, min_cell_height)
src = """
(function(){
Retina.add_renderer({ name: 'heatmap', resource: '""" + self.renderer_resource + """', filename: 'renderer.heatmap.js' });
Retina.load_renderer('heatmap').then( function () {
window."""+hname+""" = Retina.Renderer.create('heatmap', {""" + opt + """} );
window."""+hname+""".render();
});
})();
"""
if onclick:
click_func = """
var sel_rows = window."""+hname+""".selectedRows();
var row_names = """+rows+""";
var sel_names = [];
for (var i=0; i<row_names.length; i++) {
if (sel_rows[i]) {
sel_names.push(row_names[i]);
}
}
ipy.write_cell(ipy.add_cell(),\""""+onclick+""""\");"""
if onclick:
html += "<button type='button' onclick='"+click_func+"'>sub-select rows</button>"
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
if self.debug:
print html, src
else:
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
def table(self, width=None, height=None, target="", data=None, rows_per_page=20, sortcol=0, sortdir="asc", sorttype={}, sort_autodetect=True, filter_autodetect=True, filter_autodetect_select_max=10, issorted=False, offset=0, invisible_columns={}, disable_sort={}, filtertypes={}, hide_options=False, editable={}):
"""Table Renderer
Displays a browsable, filterable table with clickable cells / rows.
Options
target (HTML Container Element)
Element to render the table in.
width (INT)
Width of the table.
height (INT)
Height of the table.
rows_per_page (INT)
The maximum number of table rows to be displayed at a time. Default is 10.
sortcol (INT)
Zero based index of the row the table should be sorted by. Default is 0.
sorted (BOOLEAN)
Enables / disabled initial sorting of the table by the sortcol. Default is false.
offset (INT)
Initial first row to display. Default is 0.
invisible_columns (HASH)
Hash of column indices pointing at 1. Columns in this hash are not displayed.
disable_sort (HASH)
Hash of column indices pointing at 1. Columns in this hash can not be sorted.
sorttype (HASH)
Hash of column indices pointing at a sorttype. A sorttype can be either string or number.
filter_autodetect (BOOLEAN)
If set to false will try to detect which filter type is most appropriate for each column. Default is false.
filter_autodetect_select_max (INT)
Maximum number of distinct entries in a column that will still autodetec the column filter as a select box. Default is 10.
sort_autodetect (BOOLEAN)
If set to true will try to detect which sorttype is appropriate for each column. Default is false.
filter (HASH)
Hash of column indices pointing at filter objects. A filter object has the properties
searchword - the current entry in the search field
case_sensitive - boolean to turn on / off case sensitivity in filtering
operator - list of operators available in this filter
active_operator - selected operator
type - text or select
hide_options (BOOLEAN)
Turns display of the options button on and off. Default is false (the option button is visible).
onclick (FUNCTION)
The function to be called when the table is clicked. This function will be passed the parameters (as an ordered list)
clicked_row - array of contents of the cells of the clicked row
clicked_cell - content of the clicked cell
clicked_row_index - zero based index of the clicked row
clicked_cell_index - zero based index of the clicked cell
"""
if not target:
target = 'div_table_'+ipyTools.random_str()
html = "<div id='%s'></div>"%(target)
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
if data is None:
data = "Retina.RendererInstances.table[0].exampleData()"
else:
data = json.dumps(data)
invisible_columns = json.dumps(invisible_columns)
disable_sort = json.dumps(disable_sort)
sorttype = json.dumps(sorttype)
editable = json.dumps(editable)
width = "null" if width is None else str(width)
height = "null" if height is None else str(height)
opt = "target: document.getElementById('%s'), width: %s, height: %s, rows_per_page: %s, sortcol: %s, sorted: %s, offset: %s, invisible_columns: %s, disable_sort: %s, sortdir: '%s', sorttype: %s, filter_autodetect: %s, filter_autodetect_select_max: %s, sort_autodetect: %s, filter: %s, hide_options: %s, editable: %s, data: %s"%(target, width, height, rows_per_page, sortcol, self._bool(issorted), offset, invisible_columns, disable_sort, sortdir, sorttype, self._bool(filter_autodetect), filter_autodetect_select_max, self._bool(sort_autodetect), filtertypes, self._bool(hide_options), editable, data)
src = """
(function(){
Retina.add_renderer({ name: 'table', resource: '""" + self.renderer_resource + """', filename: 'renderer.table.js' });
Retina.load_renderer('table').then( function () { Retina.Renderer.create('table', {""" + opt + """} ).render(); } );
})();
"""
if self.debug:
print src
else:
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
def graph(self, width=800, height=400, btype="column", target="", data=None, title="", x_labels=[], x_title="", y_title="", show_legend=False, legend_position='left', title_color="black", x_title_color="black", y_title_color="black", x_labels_rotation="0", x_tick_interval=0, y_tick_interval=30, x_labeled_tick_interval=1, y_labeled_tick_interval=5, default_line_color="black", default_line_width=1, chartArea=None, legendArea=None, onclick=None):
"""Graph Renderer
Displays a graph of pie / bar charts with an optional legend.
Options
btype (STRING)
Defines the display type of the graph, can be one of
pie
column
stackedColumn
row
stackedRow
line
Default is column.
title (STRING)
Title string written at the top of the graph
title_color (CSS Color Value)
Color of the title text. Default is black.
x_title (STRING)
Title written below the x-axis.
y_title (STRING)
Title written to the left of the y-axis.
x_title_color (CSS Color Value)
Color of the x-axis title string. Default is black.
y_title_color (CSS Color Value)
Color of the y-axis title string. Default is black.
x_labels (ARRAY of STRING)
List of the labels at the ticks of the x-axis.
x_labels_rotation (STRING)
A string representing the number of degrees to rotate the labels on the x-axis. Default is 0.
y_labels (ARRAY of STRING)
List of the labels at the ticks of the y-axis. If no list is passed will use the y-valus.
x_tick_interval (INT)
Determines how many ticks are actually drawn on the x-axis. Default is 0.
y_tick_interval (INT)
Determines how many ticks are actually drawn on the y-axis. Default is 30.
x_labeled_tick_interval (INT)
Determines which ticks on the x-axis get labels. Default is 1.
y_labeled_tick_interval (INT)
The number of y-axis ticks that get labels. Default is 5.
default_line_color (CSS Color Value)
Determines the color of lines if not specified for an individual line. Default is black.
default_line_width (INT)
Number of pixels lines should be wide if not specified for an individual line. Default is 1.
show_legend (BOOLEAN)
Turns the display of the legend on / off. Default ist true.
legend_position (STRING)
Can be one of
left
right
top
bottom
chartArea (ARRAY of FLOAT)
The values passed correspond to the left, top, width and height margin of the chart area respectively. The position is relative to the top left corner of the containing div. Values less than 1 are interpreted as fractions. Values greater than 1 are interpreted as absolute pixel values.
legendArea (ARRAY of FLOAT)
If this parameter is set, the legend_position parameter will not be used. Instead pass an array of floats. The values correspond to the left, top, right and bottom margin of the legend area respectively. The position is relative to the top left corner of the containing div. Values less than 1 are interpreted as fractions. Values greater than 1 are interpreted as absolute pixel values.
width (INT)
The width of the graph in pixel (including legend).
height (INT)
The height of the graph in pixel (including legend).
data (ARRAY of OBJECT)
List of data series. Each series has a name and a data attribute. The data attribute is a list of y-values for the series.
onclick (FUNCTION)
The passed function will be called when a bar / pie slice is clicked. It will receive an object with the attributes
series - the name of the series this bar belongs to
value - the value of the bar
label - the label of the bar
item - the svg element that was clicked
index - the zero based index of this bar within its series
series_index - the zero based index of this series
"""
if not target:
target = 'div_graph_'+ipyTools.random_str()
html = "<div id='%s'></div>"%(target)
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
if len(x_labels) == 0:
x_labels = [""]
if data is None:
title = "Browser Usage"
x_labels = "['2005','2006','2007','2008']"
data = "Retina.RendererInstances.graph[0].exampleData()"
onclick = "'clickedCell = '+ JSON.stringify(params)"
else:
data = json.dumps(data)
x_labels = json.dumps(x_labels)
opt = "width: %d, height: %d, type: '%s', target: document.getElementById('%s'), data: %s, title: '%s', x_labels: %s, x_title: '%s', y_title: '%s', show_legend: %s, legend_position: '%s', title_color: '%s', x_title_color: '%s', y_title_color: '%s', x_labels_rotation: '%s', x_tick_interval: %f, y_tick_interval: %f, x_labeled_tick_interval: %f, y_labeled_tick_interval: %f, default_line_color: '%s', default_line_width: %d"%(width, height, btype, target, data, title, x_labels, x_title, y_title, self._bool(show_legend), legend_position, title_color, x_title_color, y_title_color, x_labels_rotation, x_tick_interval, y_tick_interval, x_labeled_tick_interval, y_labeled_tick_interval, default_line_color, default_line_width)
if chartArea:
opt += ", chartArea: "+json.dumps(chartArea)
if legendArea:
opt += ", legendArea: "+json.dumps(legendArea)
if onclick:
onclick = ", onclick: function(params){ipy.write_cell(ipy.add_cell(),"+onclick+");}"
else:
onclick = ""
src = """
(function(){
Retina.add_renderer({"name": "graph", "resource": '""" + self.renderer_resource + """', "filename": "renderer.graph.js" });
Retina.load_renderer("graph").then( function () { Retina.Renderer.create('graph', {""" + opt + onclick + """}).render(); });
})();
"""
if self.debug:
print src
else:
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
def plot(self, width=800, height=400, target="", data=None, title="", show_legend=True, legend_position='right', connected=True, show_dots=True, x_min=0, x_max=100, y_min=0, y_max=100, x_title="", y_title=""):
""" Plot Renderer
Displays a two dimensional plot.
Options
title (STRING)
Title string written at the top of the plot
title_color (CSS Color Value)
Color of the title text. Default is black.
default_line_color (CSS Color Value)
Determines the color of lines if not specified for an individual line. Default is black.
default_line_width (INT)
Number of pixels lines should be wide if not specified for an individual line. Default is 1.
width (INT)
The width of the graph in pixel (including legend).
height (INT)
The height of the graph in pixel (including legend).
show_dots (BOOLEAN)
display circles at the data points (for connected mode only)
connected (BOOLEAN)
connect the dots. This will disable the shape attribute of the series.
data (OBJECT)
'series' (ARRAY of OBJECT)
'name' (STRING) - name of the series
'color' (CSS Color value) - color of the series
'shape' [ 'cicrle', 'triangle', 'square' ] - shape of the points (connected==false only)
'points' (ARRAY of OBJECT)
'x' (FLOAT) - x coordinate
'y' (FLOAT) - y coordinate
show_legend (BOOLEAN)
Turns the display of the legend on / off. Default ist true.
legend_position (STRING)
Can be one of
left
right
top
bottom
x_min (FLOAT)
minimum x value
y_min (FLOAT)
minimum y value
x_max (FLOAT)
maximim x value
y_max (FLOAT)
maximum y value
x_title (STRING)
title of the x axis
y_title (STRING)
title of the y axis
"""
if not target:
target = 'div_plot_'+ipyTools.random_str()
html = "<div id='%s'></div>"%(target)
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
if data is None:
title = "Sine"
data = "Retina.RendererInstances.plot[0].exampleData()"
else:
data = json.dumps(data)
opt = "width: %d, height: %d, target: document.getElementById('%s'), data: %s, title: '%s', show_legend: %s, legend_position: '%s', connected: %s, show_dots: %s, x_min: %f, x_max: %f, y_min: %f, y_max: %f, x_title: '%s', y_title: '%s'"%(width, height, target, data, title, self._bool(show_legend), legend_position, self._bool(connected), self._bool(show_dots), x_min, x_max, y_min, y_max, x_title, y_title)
src = """
(function(){
Retina.add_renderer({"name": "plot", "resource": '""" + self.renderer_resource + """', "filename": "renderer.plot.js" });
Retina.load_renderer("plot").then( function () { Retina.Renderer.create('plot', {""" + opt + """}).render(); });
})();
"""
if self.debug:
print src
else:
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
def metagenome(self, view='summary_chart', annotation='organism', level='domain', source='Subsystems', kmer='abundance', widget=None, arg_list=False, target=None):
"""Displays Metagenome Overview Widget visualizations in given target based on given widget function and name."""
if not widget:
sys.stderr.write("Error: No metagenome widget name provided\n")
return
function, viz_type = '', ''
sub_ann = ''
if annotation == 'organism':
annotation = 'taxonomy'
sub_ann = level
elif annotation == 'function':
annotation = 'ontology'
sub_ann = source
if view == 'summary_chart':
function, viz_type = 'summary_piechart('+widget+'.index)', 'graph'
elif view == 'summary_stats':
function, viz_type = 'analysis_statistics('+widget+'.index)', 'paragraph'
elif view == 'annotation_chart':
function, viz_type = 'annotation_piechart('+widget+'.index, '+annotation+', '+sub_ann+')', 'graph'
elif view == 'bp_histogram':
function, viz_type = 'bp_areagraph('+widget+'.index)', 'graph'
elif (view == 'drisee') or (view == 'kmer') or (view == 'rarefaction'):
function, viz_type = 'mg_plot('+widget+'.index, "'+view+'", "'+kmer+'")', 'plot'
elif view == 'rank_abundance':
function, viz_type = 'taxon_linegraph('+widget+'.index, "'+level+'", 50)', 'graph'
elif view == 'mixs':
function, viz_type = 'mixs_metadata('+widget+'.index, true)', 'paragraph'
elif view == 'metadata':
function, viz_type = 'metadata_table('+widget+'.index)', 'table'
else:
sys.stderr.write("No visualization available for type '%s'\n"%view)
return
html = None
if not target:
target = 'mg_'+view+'_'+ipyTools.random_str()
if arg_list:
clean_obj = ""
if viz_type == 'graph':
clean_obj = target+".btype = "+target+".type; delete "+target+".type;"
elif viz_type == 'table':
clean_obj = target+".issorted = "+target+".sorted; delete "+target+".sorted; "
clean_obj += target+".filtertypes = "+target+".filter; delete "+target+".filter;"
src = """
(function(){
var """+target+""" = """+widget+"""."""+function+"""; """+clean_obj+"""
var ipy_cmd = JSON.stringify("""+target+""").replace("true", "True").replace("false", "False");
var new_idx = ipy.add_cell(undefined, 'code', 'above');
ipy.write_cell(new_idx, '"""+target+""" = '+ipy_cmd);
ipy.execute_cell(new_idx);
})();
"""
else:
html = "<div id='%s'></div>"%(target)
src = """
(function(){
var """+target+""" = """+widget+"""."""+function+""";
"""+target+""".target = document.getElementById('"""+target+"""');
Retina.load_renderer(\""""+viz_type+"""\").then( function () {
Retina.Renderer.create('"""+viz_type+"""', """+target+""").render();
});
})();
"""
if self.debug:
print src
else:
if html:
IPython.core.display.display_html(IPython.core.display.HTML(data=html))
IPython.core.display.display_javascript(IPython.core.display.Javascript(data=src))
