ó WáWc@sÝdZddlZejdƒidd6ZejdeddljZddlj Z ddl j Z ddlmZmZddljjZddlZddlZddlZd„Zd „Zd „Zd „ZdS( s@ Created on 2015-03-27 @author: Ian McDowell, Dinesh Manandhar iÿÿÿÿNtAggitsizetfont(tlinkaget dendrogramcCs«xF|jjƒD]5\}}||kr8|jdƒq|jdƒqWd|krh|jjdƒn|jjgƒd|kr—|jjdƒn|jjgƒdS(so see matplotlib examples: http://matplotlib.org/examples/pylab_examples/spine_placement_demo.html toutwardi tnonetlefttbottomN(Ri (tspinestitemst set_positiont set_colortyaxistset_ticks_positiont set_tickstxaxis(taxR tloctspine((s DP_GP/plot.pyt adjust_spiness   cCsët|ƒ}t|ƒ}d} ttj|t| ƒƒƒ} d} tj| | ƒ} gtdt|ƒ| ƒD]} || | | !^qo}d}xRt|ƒD]D\}}tj dddd5d d d d d dƒ}xÉt|ƒD]»\} }|j | | | dƒ}tj tj t|ƒt|ƒddƒƒ}||jj|dtd||jjƒ\}}tj|jddƒƒ}|dd…df}tjjjj|||d|d|d|dd|ƒ|jt|ƒt|ƒfƒ|s |jd6ƒntjdddddddƒxGt||jƒD]2}|j |tj!|j"|ƒddddƒq<W|j ||ddƒt#j$ddgddd d d dd!ddd"ƒ}t%j&ggddd#d$ƒ}|j'|j(d||gd%d&d$gd'd(d)td*idd+6ƒt)|d,d-gƒ|d.krJ|j*d/ƒn|j*d0|ƒ|j+|ƒ|j,|ƒ|j-d1ƒ|j.d2|ƒ|d7}qâWtj/ƒx5|D]-}tj0|d3t1|dƒd4|ƒq²WqŸWdS(7s Plot gene expression over a time course with a panel for each cluster. Each panel contains transparent red lines for the expression of each individual gene within the cluster, the cluster mean, and a ribbon twice the standard deviation about the cluster mean. This is essentially a wrapper function for GPy.plotting.matplot_dep.base_plots.gpplot. :param clusters: dictionary of dp_cluster objects :type clusters: dict :param gene_expression_matrix: expression over timecourse of dimension |genes|x|timepoints| :type gene_expression_matrix: pandas dataframe :param t: sampled timepoints :type t: numpy array of floats :param time_unit: time units in reference to t, e.g. 'days','hr.','min.','sec.' :type t: str :param output_path_prefix: absolute path to output :type output_path_prefix: str :param plot_types: plots to be generated, e.g. ['png','pdf','svg'] or simply ['png'] :type plot_types: list of strings :rtype: None (output is saved to file(s)) iiiitnumtfigsizeii tdpii,t facecolortwt edgecolortkiôtfull_covtkerntaxisNgà?Riýÿÿÿitcolortblacktlss--talphatredgš™™™™™¹?tblues#33CCFFtlwg333333Ó?tlabelsindividual gene trajectorys cluster meanucluster mean ± 2 x std. dev.RitframeontpropRRRttTimes Time in %ssGene expressions Cluster %st_gene_expression_fig_t.(ii (iýÿÿÿi(2tsortedtlentinttnptceiltfloattxranget enumeratetplttfiguretNonet add_subplottvstacktlinspacetmintmaxtmodeltpredicttFalseRthstacktmeantGPytplottingt matplot_dept base_plotstgpplottset_xlimtset_ylimtaxhlinetlisttmemberstplottarraytixtmpatchest RectangletmlinestLine2DtlegendtlinesRt set_xlabelt set_xtickstset_xticklabelst set_ylabelt set_titlet tight_layouttsavefigtstr(tclusterstgene_expression_matrixttt time_unittoutput_path_prefixt plot_typestdo_not_mean_centertIDsttotal_subplotstsubplots_per_figttotal_no_of_figst total_colst total_rowstit IDs_splittindextctfigtIDRtXgridtmutvtgenetlight_blue_patchtred_linet plot_type((s DP_GP/plot.pytplot_cluster_gene_expression-sR  6*-2=03      cCsd|}tjdgƒtjddƒ}|jddddgƒ}tj|d d ƒ}tj|d d d tjƒ}|j gƒ|j gƒ|j dƒ|jddddgƒ}tj|d tjƒ} tjdgƒ|j gƒ|j gƒ|j dƒ|jddddgƒ} |d} | d} || dd…f}|dd…| f}| j |dddddtj jƒ} | j gƒ| j gƒ|jddddgƒ}tj| d|ƒ|jddddƒx)|D]!}tj|d|ddƒqòW| S(sí Plot the posterior similarity matrix as heatmap with dendrogram. dim(S) = n x n, where n = total number of genes. S[i,j] = (# samples gene i in cluster with gene j)/(# total samples) Hierarchically cluster by complete linkage for orderliness of visualization. Although of questionable usefulness, function returns all gene names in the order in which they were clustered. This list might be used to visually inspect heatmap, yet heatmap is largely intended for high-level view of data. :param sim_mat: sim_mat[i,j] = (# samples gene i in cluster with gene j)/(# total samples) :type sim_mat: numpy array of (0-1) floats :param output_path_prefix: absolute path to output :type output_path_prefix: str :param plot_types: plots to be generated, e.g. ['png','pdf','svg'] or simply ['png'] :type plot_types: list of strings :rtype: array-like, names of genes in order of clustering (both left to right and top to bottom) iR Riig{®Gáz”?gš™™™™™É?g333333ã?tmethodtcompletet orientationtrighttcolor_thresholdtofftleavesNtaspecttautotorigintlowertcmapgìQ¸…ëé?tcaxtwspacethspaces%_posterior_similarity_matrix_heatmap.t bbox_inches(ii(tschtset_link_color_paletteR5R6tadd_axesRRR0tinfRVt set_yticksRtmatshowtcmtbinarytcolorbartsubplots_adjustR[(tsim_matRaRbtdist_matRntax1tYtZ1tax2tZ2taxmatrixtidx1tidx2timtaxcolorRv((s DP_GP/plot.pytplot_similarity_matrix€s:         '   c Cs|ddd…f}|dd…dd…fjdƒ}tj|ƒ|}tttj|ƒƒtt|ƒƒƒ}i} xZ|D]R} tj|| kƒ\} } tj | ƒ} | j dƒ\\}}|| | s         S B