Ri4dZddlmZddlmZGddZy)zGraph module. Provides: - GraphData - Contains data from which a graph will be drawn, and information about its presentation For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com )sqrt)colorsc eZdZdZddddej ej dddf dZdZdZ dZ dZ d Z d Z d Zd Zd ZdZy) GraphDataaGraph Data. Attributes: - id Unique identifier for the data - data Dictionary of describing the data, keyed by position - name String describing the data - style String ('bar', 'heat', 'line') describing how to draw the data - poscolor colors.Color for drawing high (some styles) or all values - negcolor colors.Color for drawing low values (some styles) - linewidth Int, thickness to draw the line in 'line' styles Nbarc ||}| | }||_i|_||j|||_||_||_||_d|_||_y)aInitialize. Arguments: - id Unique ID for the graph - data List of (position, value) tuples - name String describing the graph - style String describing the presentation style ('bar', 'line', 'heat') - color colors.Color describing the color to draw all or the 'high' (some styles) values (overridden by backwards compatible argument with UK spelling, colour). - altcolor colors.Color describing the color to draw the 'low' values (some styles only) (overridden by backwards compatible argument with UK spelling, colour). - center Value at which x-axis crosses y-axis. N) iddataset_datanamestyleposcolornegcolor linewidthcenter) selfr r r rcoloraltcolorrcolour altcolours Y/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py__init__zGraphData.__init__,sf<  E   H   MM$       c6|D]\}}||j|<y)z/Add data as a list of (position, value) tuples.Nr )rr posvals rr zGraphData.set_data\s" !HC DIIcN !rcg}|jD]$}|j|}|j||f&|j|S)z9Return data as a list of sorted (position, value) tuples.)r appendsort)rr xvalyvals rget_datazGraphData.get_dataasGII &D99T?D KKt % &  rc,|\}}||j|<y)zCAdd a single point to the set of data as a (position, value) tuple.Nr)rpointrrs r add_pointzGraphData.add_pointjsS #rct|jj}t|}|d||dz||dz|d|zdz|dfS)zCReturn (minimum, lowerQ, medianQ, upperQ, maximum) values as tuple.rr )sortedr valueslen)rr datalens r quartileszGraphData.quartilesoscdii&&()d) G A  A  W! " H   rc@t|j}|d|dfS)zReturn range of data as (start, end) tuple. Returns the range of the data, i.e. its start and end points on the genome as a (start, end) tuple. rr+)r,r )r positionss rrangezGraphData.range{s' 499% ! im,,rcvt|jj}t|t |z S)z2Return the mean value for the data points (float).)listr r-sumr.)rr s rmeanzGraphData.means,DII$$&'4y3t9$$rct|jj}|j}d}|D] }|||z dzz }t |t |dz z S)z:Return the sample standard deviation for the data (float).gr )r5r r-r7rr.)rr mruntotalentrys rstdevzGraphData.stdevseDII$$&' IIK )E q( (H )HD A .//rc,t|jS)z,Return the number of points in the data set.)r.r )rs r__len__zGraphData.__len__s499~rc|t|tr|j|St|tr|j}|j }|j |j dk7rtg}t|jD].}||k\s ||ks|j||j|f0|Std)a@Return data value(s) at the given position. Given an integer representing position on the sequence returns a float - the data value at the passed position. If a slice, returns graph data from the region as a list or (position, value) tuples. Slices with step are not supported. r9zNeed an integer or a slice) isinstanceintr slicestartstopstep ValueErrorr,r TypeError)rindexlowhighoutlistrs r __getitem__zGraphData.__getitem__s eS !99U# # u %++C::Dzz%%**/  Gdii( :#:#+NNC3#89 :N89 9rcd|jd|jg}|jdt|jz|jd|j |jd|j d|jd|jz|jd|jzd j|S) z*Return a string describing the graph data.z GraphData: z, ID: zNumber of points: %dzMean data value: z Sample SD: z.3fz,Minimum: %s 1Q: %s 2Q: %s 3Q: %s Maximum: %szSequence Range: %s..%s ) r r r r.r r7r=r0r3join)routstrs r__str__zGraphData.__str__s!$))F477)<= ,s499~=> )$))+78 DJJL#567 >AQ Q   .=>yy  r)__name__ __module__ __qualname____doc__r lightgreen darkseagreenrr r$r'r0r3r7r=r?rMrRrrrrsh    $$.`!    -% 0:4 !rrN)rVmathr reportlab.librrrYrrr\s a!a!r