How to use the seaborn.heatmap function in seaborn

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github smu160 / PvsNP / analysis_utils.py View on Github external
heatmap
        size: the size of the heatmap to be plotted, default is 16
    """

    # Generate a mask for the upper triangle
    mask = np.zeros_like(dataframe.corr(), dtype=np.bool)
    mask[np.triu_indices_from(mask)] = True

    # Set up the matplotlib figure
    _, _ = plt.subplots(figsize=(size, size))

    # Generate a custom diverging colormap
    cmap = sns.diverging_palette(220, 10, as_cmap=True)

    # Draw the heatmap with the mask and correct aspect ratio
    sns.heatmap(dataframe.corr(), mask=mask, cmap=cmap, vmax=1.0, center=0, square=True, linewidths=.5, cbar_kws={"shrink": .5})
github pyprob / pyprob / pyprob / analytics.py View on Github external
table.add_row(FootnoteText('Length'), FootnoteText('{:,}'.format(len(trace_addresses))))
                            doc.append('\n')

                            im = np.zeros((addresses, len(trace_addresses)))
                            for i in range(len(trace_addresses)):
                                address = trace_addresses[i]
                                address_i = plt_addresses.index(address)
                                im[address_i, i] = 1
                            truncate = 100
                            for col_start in range(0, len(trace_addresses), truncate):
                                col_end = min(col_start + truncate, len(trace_addresses))
                                with doc.create(Figure(position='H')) as plot:
                                    fig = plt.figure(figsize=(20 * ((col_end + 4 - col_start) / truncate),4))
                                    ax = plt.subplot(111)
                                    # ax.imshow(im,cmap=plt.get_cmap('Greys'))
                                    sns.heatmap(im[:,col_start:col_end], cbar=False, linecolor='lightgray', linewidths=.5, cmap='Greys',yticklabels=plt_addresses,xticklabels=np.arange(col_start,col_end))
                                    plt.yticks(rotation=0)
                                    fig.tight_layout()
                                    plot.add_plot(width=NoEscape(r'{0}\textwidth'.format((col_end + 4 - col_start) / truncate)), placement=NoEscape(r'\raggedright'))

                            with doc.create(Figure(position='H')) as plot:
                                pairs = {}
                                for left, right in zip(trace_addresses, trace_addresses[1:]):
                                    if (left, right) in pairs:
                                        pairs[(left, right)] += 1
                                    else:
                                        pairs[(left, right)] = 1

                                fig = plt.figure(figsize=(10,5))
                                ax = plt.subplot(111)
                                graph = pydotplus.graphviz.graph_from_dot_data(master_graph.to_string())
github tlatkowski / multihead-siamese-nets / debug / vis.py View on Github external
def attention_visualization(att):
    sns.heatmap(att[0, :, :])
    plt.show()
github veronicachelu / temporal_abstraction / subgoal_discovery / agents / dqn_sf_base_agent.py View on Github external
def plot_eigenoptions(self, folder, sess):
    # feed_dict = {self.orig_net.matrix_sf: self.matrix_sf}
    # s, v = sess.run([self.orig_net.s, self.orig_net.v], feed_dict=feed_dict)
    u, s, v = np.linalg.svd(self.matrix_sf, full_matrices=False)
    eigenvalues = s
    eigenvectors = v
    # U, s, V = np.linalg.svd(matrix)
    S = np.diag(s[1:])
    sr_r_m = np.dot(u[:, 1:], np.dot(S, v[1:]))
    import seaborn as sns
    sns.plt.clf()
    ax = sns.heatmap(sr_r_m, cmap="Blues")
    ax.set(xlabel='SR_vect_size=128', ylabel='Grid states/positions')
    folder_path = os.path.join(os.path.join(self.config.stage_logdir, "summaries"), "eigenoptions")
    tf.gfile.MakeDirs(folder_path)
    sns.plt.savefig(os.path.join(folder_path, 'reconstructed_sr.png'))
    sns.plt.close()

    folder_path = os.path.join(os.path.join(self.config.stage_logdir, "summaries"), folder)
    tf.gfile.MakeDirs(folder_path)

    # variance_eigenvectors = []
    # for i in range(self.nb_states):
    #   variance_eigenvectors.append([])
    # for i in range(self.nb_states):
    #   variance_eigenvectors[i].append(np.var(eigenvectors[:, i]))
    #   sns.plt.clf()
    #   sns.plt.plot(variance_eigenvectors[i])
github stanfordnlp / mac-network / visualization.py View on Github external
# xx = np.arange(0, len(x), 1)
    # yy = np.arange(0, len(y), 1)
    # extent2 = np.min(xx), np.max(xx), np.min(yy), np.max(yy)
    
    fig2, bx = plt.subplots(1, 1) # figsize = figureTableDims
    bx.cla()

    sns.set(font_scale = fontScale)

    if args.trans:
        table = np.transpose(table)
        x, y = y, x
    
    tableMap = pandas.DataFrame(data = table, index = x, columns = y)
    
    bx = sns.heatmap(tableMap, cmap = "Purples", cbar = False, linewidths = .5, linecolor = "gray", square = True)
    
    # x ticks
    if args.trans:
        bx.xaxis.tick_top()
    locs, labels = plt.xticks()
    if args.trans:
        plt.setp(labels, rotation = 0)
    else:
        plt.setp(labels, rotation = 60)

    # y ticks
    locs, labels = plt.yticks()
    plt.setp(labels, rotation = 0)

    plt.savefig(outTableAttName(instance, name), dpi = 720)
github hbc / projects / tanzi_ad / scripts / sv_summarize.py View on Github external
def _plot_heatmap(call_csv, samples, positions, sample_info, batch_counts):
    def sample_sort(x):
        batch = sample_info[x]["batch"]
        return (-batch_counts.get(batch, 0), batch, x)
    out_file = "%s.png" % os.path.splitext(call_csv)[0]
    df = pd.read_csv(call_csv)
    sv_rect = df.pivot(index="position", columns="sample", values="caller_support")
    sv_rect = sv_rect.reindex_axis(positions, axis=0)
    sv_rect = sv_rect.reindex_axis(["%s: %s" % (sample_info[x]["batch"], x)
                                    for x in sorted(samples, key=sample_sort)],
                                   axis=1)
    fig = plt.figure(tight_layout=True)
    plt.title("Shared structural variant calls for affected and unaffected in regions of interest",
              fontsize=16)
    ax = sns.heatmap(sv_rect, cbar=False,
                     cmap=sns.diverging_palette(255, 1, n=3, as_cmap=True))
    colors = sns.diverging_palette(255, 1, n=3)
    b1 = plt.bar(0, 0, bottom=-100, color=colors[-1])
    b2 = plt.bar(0, 0, bottom=-100, color=colors[0])
    ax.legend([b1, b2], ["affected", "unaffected"], ncol=2,
              bbox_to_anchor=(0.85, 0.995), loc=3)
    plt.setp(ax.get_xticklabels(), fontsize=8)
    plt.setp(ax.get_yticklabels(), fontsize=8)
    fig.set_size_inches(20, 8)
    fig.savefig(out_file)
github nextgenusfs / funannotate / lib / library.py View on Github external
def drawHeatmap(df, color, output, labelsize, annotate):
    with warnings.catch_warnings():
        warnings.simplefilter('ignore')
        import matplotlib
        matplotlib.use('Agg')
        import matplotlib.pyplot as plt
        import seaborn as sns
    #get size of table
    width = len(df.columns) / 2
    height = len(df.index) / 4
    fig, ax = plt.subplots(figsize=(width,height))
    cbar_ax = fig.add_axes(shrink=0.4)
    if annotate:
        sns.heatmap(df,linewidths=0.5, cmap=color, ax=ax, fmt="d", annot_kws={"size": 4}, annot=True)
    else:
        sns.heatmap(df,linewidths=0.5, cmap=color, ax=ax, annot=False)
    plt.yticks(rotation=0)
    plt.xticks(rotation=90)
    for item in ax.get_xticklabels():
        item.set_fontsize(8)
    for item in ax.get_yticklabels():
        item.set_fontsize(int(labelsize))
    fig.savefig(output, format='pdf', dpi=1000, bbox_inches='tight')
    plt.close(fig)
github hammerlab / cohorts / cohorts / landscape_plot.py View on Github external
def _indicator_plot(data,
                   sample_col,
                   indicator_col,
                   colormap=None,
                   figsize=None,
                   ax=None):
    indicator_data = data.set_index([sample_col])[[indicator_col]].T
    indicator_plot = sb.heatmap(indicator_data,
               square=True,
               cbar=None,
               xticklabels=True,
               linewidths=1,
               cmap=colormap,
               ax=ax)
    plt.setp(indicator_plot.axes.get_yticklabels(), rotation=0)
    return indicator_plot
github fancompute / wavetorch / wavetorch / plot.py View on Github external
pal2 = sns.blend_palette(["#f7f7f7", "#fddbc7", "#f4a582", "#d6604d", "#b2182b", "#67001f"], as_cmap=True)

	sns.heatmap(cm.transpose(),
				fmt=fmt,
				annot=True,
				cmap=pal1,
				linewidths=0,
				cbar=False,
				mask=mask1,
				ax=ax,
				xticklabels=labels,
				yticklabels=labels,
				square=True,
				annot_kws={'size': 'small'})

	sns.heatmap(cm.transpose(),
				fmt=fmt,
				annot=True,
				cmap=pal2,
				linewidths=0,
				cbar=False,
				mask=mask2,
				ax=ax,
				xticklabels=labels,
				yticklabels=labels,
				square=True,
				annot_kws={'size': 'small'})

	for _, spine in ax.spines.items():
		spine.set_visible(True)
	ax.set_xlabel('Input')
	ax.set_ylabel('Predicted')
github spatialucr / geosnap / geosnap / visualize / seq.py View on Github external
cluster_i_temp_sort = np.sort(cluster_i_temp, order=years)
            cluster_i_temp_sort = np.array(list(map(list, cluster_i_temp_sort)))
            if not cluster_i_temp_sort.shape[0]:
                ax.set_axis_off()
                continue
            elif cluster_i_temp_sort.shape[0] < max_cluster:
                diff_n = max_cluster - cluster_i_temp_sort.shape[0]
                bigger = np.unique(cluster_i_temp_sort).max()+1
                cluster_i_temp_sort = np.append(cluster_i_temp_sort, np.zeros(
                    (diff_n, cluster_i_temp_sort.shape[1]))+bigger, axis=0)
            df_cluster_i_temp_sort = pd.DataFrame(cluster_i_temp_sort,
                                                  columns=years)

            if cluster_i_temp.shape[0] == max_cluster:
                cbar_ax = fig.add_axes([0.3, -0.02, 0.42, 0.02])
                ax = sns.heatmap(df_cluster_i_temp_sort, ax=ax, cmap=cluster_cmap,
                                 cbar_kws={"orientation": "horizontal"},
                                 cbar_ax=cbar_ax)
                colorbar = ax.collections[0].colorbar
                colorbar.set_ticks(np.linspace(min(neighborhood) + 0.5, max(neighborhood) - 0.5, k))
                colorbar.set_ticklabels(neighborhood)
            else:
                ax = sns.heatmap(df_cluster_i_temp_sort, ax=ax, cmap=my_cmap,
                                 cbar=False)


    plt.tight_layout()
    # fig.tight_layout(rect=[0, 0, .9, 1])
    if save_fig:
        dirName = "figures"
        if not path.exists(dirName):
            mkdir(dirName)