Mercurial > repos > mheinzl > fsd
changeset 41:54f0dac1c834 draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty
| author | mheinzl |
|---|---|
| date | Wed, 14 Aug 2019 04:30:58 -0400 |
| parents | 948064d8714e |
| children | 321a4871564b |
| files | fsd.py fsd.xml test-data/fsd_output1.pdf test-data/fsd_output2.pdf |
| diffstat | 4 files changed, 11 insertions(+), 13 deletions(-) [+] |
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--- a/fsd.py Wed Jul 24 05:50:06 2019 -0400 +++ b/fsd.py Wed Aug 14 04:30:58 2019 -0400 @@ -114,7 +114,9 @@ fig.text(0.45, 0.11, legend3b, size=10, transform=plt.gcf().transFigure) fig2.text(0.45, 0.11, legend3b, size=10, transform=plt.gcf().transFigure) - legend4 = "family size > 20:\nnr. of tags\n{:,} ({:.3f})".format(numpy.bincount(data1)[len(numpy.bincount(data1)) - 1].astype(int), float(numpy.bincount(data1)[len(numpy.bincount(data1)) - 1]) / len(data1)) + legend4 = "family size > 20:\nnr. of tags\n{:,} ({:.3f})".format(len(integers[integers > 20]), + float(sum(integers[integers > 20])) + / sum(integers)) fig.text(0.58, 0.11, legend4, size=10, transform=plt.gcf().transFigure) fig2.text(0.58, 0.11, legend4, size=10, transform=plt.gcf().transFigure) @@ -157,9 +159,7 @@ fig.text(0.45, 0.09, legend3, size=10, transform=plt.gcf().transFigure) fig2.text(0.45, 0.09, legend3, size=10, transform=plt.gcf().transFigure) - legend4 = "{:,} ({:.3f})".format( - numpy.bincount(data2)[len(numpy.bincount(data2)) - 1].astype(int), - float(numpy.bincount(data2)[len(numpy.bincount(data2)) - 1]) / len(data2)) + legend4 = "{:,} ({:.3f})".format(len(integers2[integers2 > 20]), float(sum(integers2[integers2 > 20])) / sum(integers2)) fig.text(0.58, 0.09, legend4, size=10, transform=plt.gcf().transFigure) fig2.text(0.58, 0.09, legend4, size=10, transform=plt.gcf().transFigure) @@ -202,9 +202,7 @@ fig.text(0.45, 0.07, legend3b, size=10, transform=plt.gcf().transFigure) fig2.text(0.45, 0.07, legend3b, size=10, transform=plt.gcf().transFigure) - legend4 = "{:,} ({:.3f})".format( - numpy.bincount(data3)[len(numpy.bincount(data3)) - 1].astype(int), - float(numpy.bincount(data3)[len(numpy.bincount(data3)) - 1]) / len(data3)) + legend4 = "{:,} ({:.3f})".format(len(integers3[integers3 > 20]), float(sum(integers3[integers3 > 20])) / sum(integers3)) fig.text(0.58, 0.07, legend4, size=10, transform=plt.gcf().transFigure) fig2.text(0.58, 0.07, legend4, size=10, transform=plt.gcf().transFigure) @@ -247,9 +245,7 @@ fig.text(0.45, 0.05, legend3b, size=10, transform=plt.gcf().transFigure) fig2.text(0.45, 0.05, legend3b, size=10, transform=plt.gcf().transFigure) - legend4 = "{:,} ({:.3f})".format( - numpy.bincount(data4)[len(numpy.bincount(data4)) - 1].astype(int), - float(numpy.bincount(data4)[len(numpy.bincount(data4)) - 1]) / len(data4)) + legend4 = "{:,} ({:.3f})".format(len(integers4[integers4 > 20]), float(sum(integers4[integers4 > 20])) / sum(integers4)) fig.text(0.58, 0.05, legend4, size=10, transform=plt.gcf().transFigure) fig2.text(0.58, 0.05, legend4, size=10, transform=plt.gcf().transFigure) @@ -286,6 +282,7 @@ counts_rel = ax.hist(list_to_plot2, weights=w, bins=numpy.arange(1, 23), stacked=False, edgecolor="black", linewidth=1, label=label, align="left", alpha=0.7, rwidth=0.8) + ax.set_ylim(0, 1.07) else: counts = ax.hist(list_to_plot2, bins=numpy.arange(minimumX, maximumX + 2), stacked=False, edgecolor="black", linewidth=1, label=label, align="left", alpha=0.7, rwidth=0.8, color=colors) ax.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(0.9, 1)) @@ -327,8 +324,9 @@ new_c.append(c[c_idx]) new_unique.append(unique[c_idx]) y = numpy.array(new_unique) * numpy.array(new_c) - if len([list_to_plot_original > 20]) > 0: + if sum(list_to_plot_original[i] > 20) > 0: y[len(y) - 1] = sum(list_to_plot_original[i][list_to_plot_original[i] > 20]) + # y = [y[x[idx] == unique][0] if x[idx] in unique else 0 for idx in range(len(x))] reads.append(y) reads_rel.append(list(numpy.float_(y)) / sum(y)) @@ -343,7 +341,7 @@ if to_plot[l] == "Relative frequencies": counts2_rel = ax.bar(x, list(numpy.float_(y)) / numpy.sum(y), align="edge", width=w, edgecolor="black", label=label[i],linewidth=1, alpha=0.7, color=colors[i]) - + ax.set_ylim(0, 1.07) else: y = list(y.reshape((len(y))))
--- a/fsd.xml Wed Jul 24 05:50:06 2019 -0400 +++ b/fsd.xml Wed Aug 14 04:30:58 2019 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!-- galaxy version 16.04 --> -<tool id="fsd" name="FSD" version="1.0.1"> +<tool id="fsd" name="FSD" version="1.0.2"> <description>: Family Size Distribution of duplex sequencing tags</description> <requirements> <requirement type="package" version="2.7">python</requirement>