Mercurial > repos > iuc > scanpy_plot
comparison macros.xml @ 1:e4c0f5ee8e17 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author | iuc |
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date | Wed, 16 Oct 2019 06:28:57 -0400 |
parents | 397d2c97af05 |
children | 4bfb75bb7c8e |
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0:397d2c97af05 | 1:e4c0f5ee8e17 |
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1 <macros> | 1 <macros> |
2 <token name="@version@">1.4</token> | 2 <token name="@version@">1.4.4</token> |
3 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> | 3 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> |
4 <xml name="requirements"> | 4 <xml name="requirements"> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="@version@">scanpy</requirement> | 6 <requirement type="package" version="@version@">scanpy</requirement> |
7 <requirement type="package" version="2.0.17">loompy</requirement> | 7 <requirement type="package" version="2.0.17">loompy</requirement> |
8 <requirement type="package" version="2.9.0">h5py</requirement> | |
9 <requirement type="package" version="0.7.0">leidenalg</requirement> | |
8 <yield /> | 10 <yield /> |
9 </requirements> | 11 </requirements> |
10 </xml> | 12 </xml> |
11 <xml name="citations"> | 13 <xml name="citations"> |
12 <citations> | 14 <citations> |
13 <citation type="doi">10.1186/s13059-017-1382-0</citation> | 15 <citation type="doi">10.1186/s13059-017-1382-0</citation> |
14 </citations> | 16 </citations> |
15 </xml> | 17 </xml> |
16 <xml name="version_command"> | 18 <xml name="version_command"> |
17 <version_command><![CDATA[python -c "import scanpy.api as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> | 19 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> |
18 </xml> | 20 </xml> |
19 <token name="@CMD@"><![CDATA[ | 21 <token name="@CMD@"><![CDATA[ |
22 cp '$adata' 'anndata.h5ad' && | |
20 cat '$script_file' && | 23 cat '$script_file' && |
21 python '$script_file' | 24 python '$script_file' && |
25 ls . | |
22 ]]> | 26 ]]> |
23 </token> | 27 </token> |
24 <token name="@CMD_imports@"><![CDATA[ | 28 <token name="@CMD_imports@"><![CDATA[ |
25 import scanpy.api as sc | 29 import scanpy as sc |
26 import pandas as pd | 30 import pandas as pd |
27 import numpy as np | 31 import numpy as np |
28 ]]> | 32 ]]> |
29 </token> | 33 </token> |
30 <xml name="inputs_anndata"> | 34 <xml name="inputs_anndata"> |
31 <conditional name="input"> | 35 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> |
32 <param name="format" type="select" label="Format for the annotated data matrix"> | |
33 <option value="loom">loom</option> | |
34 <option value="h5ad">h5ad-formatted hdf5 (anndata)</option> | |
35 </param> | |
36 <when value="loom"> | |
37 <param name="adata" type="data" format="loom" label="Annotated data matrix"/> | |
38 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/> | |
39 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/> | |
40 <param name="x_name" type="text" value="spliced" label="X_name"/> | |
41 <param name="obs_names" type="text" value="CellID" label="obs_names"/> | |
42 <param name="var_names" type="text" value="Gene" label="var_names"/> | |
43 </when> | |
44 <when value="h5ad"> | |
45 <param name="adata" type="data" format="h5" label="Annotated data matrix"/> | |
46 </when> | |
47 </conditional> | |
48 </xml> | 36 </xml> |
49 <token name="@CMD_read_inputs@"><![CDATA[ | 37 <token name="@CMD_read_inputs@"><![CDATA[ |
50 #if $input.format == 'loom' | 38 adata = sc.read('anndata.h5ad') |
51 adata = sc.read_loom( | |
52 '$input.adata', | |
53 sparse=$input.sparse, | |
54 cleanup=$input.cleanup, | |
55 X_name='$input.x_name', | |
56 obs_names='$input.obs_names', | |
57 var_names='$input.var_names') | |
58 #else if $input.format == 'h5ad' | |
59 adata = sc.read_h5ad('$input.adata') | |
60 #end if | |
61 ]]> | 39 ]]> |
62 </token> | 40 </token> |
63 <xml name="anndata_output_format"> | |
64 <param name="anndata_output_format" type="select" label="Format to write the annotated data matrix"> | |
65 <option value="loom">loom</option> | |
66 <option value="h5ad">h5ad-formatted hdf5 (anndata)</option> | |
67 </param> | |
68 </xml> | |
69 <xml name="anndata_modify_output_input"> | |
70 <conditional name="modify_anndata"> | |
71 <param name="modify_anndata" type="select" label="Return modify annotate data matrix?"> | |
72 <option value="true">Yes</option> | |
73 <option value="false">No</option> | |
74 </param> | |
75 <when value="true"> | |
76 <expand macro="anndata_output_format"/> | |
77 </when> | |
78 <when value="false"/> | |
79 </conditional> | |
80 </xml> | |
81 <xml name="anndata_outputs"> | 41 <xml name="anndata_outputs"> |
82 <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"> | 42 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> |
83 <filter>anndata_output_format == 'h5ad'</filter> | |
84 </data> | |
85 <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix"> | |
86 <filter>anndata_output_format == 'loom'</filter> | |
87 </data> | |
88 </xml> | |
89 <xml name="anndata_modify_outputs"> | |
90 <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"> | |
91 <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'h5ad'</filter> | |
92 </data> | |
93 <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix"> | |
94 <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'loom'</filter> | |
95 </data> | |
96 </xml> | 43 </xml> |
97 <token name="@CMD_anndata_write_outputs@"><![CDATA[ | 44 <token name="@CMD_anndata_write_outputs@"><![CDATA[ |
98 #if $anndata_output_format == 'loom' | |
99 adata.write_loom('anndata.loom') | |
100 #else if $anndata_output_format == 'h5ad' | |
101 adata.write('anndata.h5ad') | 45 adata.write('anndata.h5ad') |
102 #end if | |
103 ]]> | |
104 </token> | |
105 <token name="@CMD_anndata_write_modify_outputs@"><![CDATA[ | |
106 #if $modify_anndata.modify_anndata == 'true' | |
107 #if $modify_anndata.anndata_output_format == 'loom' | |
108 adata.write_loom('anndata.loom') | |
109 #elif $modify_anndata.anndata_output_format == 'h5ad' | |
110 adata.write('anndata.h5ad') | |
111 #end if | |
112 #end if | |
113 ]]> | 46 ]]> |
114 </token> | 47 </token> |
115 <xml name="svd_solver"> | 48 <xml name="svd_solver"> |
116 <param name="svd_solver" type="select" label="SVD solver to use" help=""> | 49 <param name="svd_solver" type="select" label="SVD solver to use" help=""> |
117 <option value="auto">Automatically chosen depending on the size of the problem</option> | 50 <option value="auto">Automatically chosen depending on the size of the problem</option> |
421 </xml> | 354 </xml> |
422 <xml name="param_use_raw"> | 355 <xml name="param_use_raw"> |
423 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/> | 356 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/> |
424 </xml> | 357 </xml> |
425 <xml name="param_log"> | 358 <xml name="param_log"> |
426 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?" help=""/> | 359 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/> |
427 </xml> | 360 </xml> |
428 <xml name="pl_figsize"> | 361 <xml name="pl_figsize"> |
429 <conditional name="figsize"> | 362 <conditional name="figsize"> |
430 <param name="test" type="select" label="Custom figure size" > | 363 <param name="test" type="select" label="Custom figure size" > |
431 <option value="yes">Yes</option> | 364 <option value="yes">Yes</option> |
471 </xml> | 404 </xml> |
472 <xml name="param_layer"> | 405 <xml name="param_layer"> |
473 <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/> | 406 <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/> |
474 </xml> | 407 </xml> |
475 <token name="@CMD_param_plot_inputs@"><![CDATA[ | 408 <token name="@CMD_param_plot_inputs@"><![CDATA[ |
476 adata=adata, | 409 adata, |
477 save='.$format', | 410 save='.$format', |
478 show=False, | 411 show=False, |
479 ]]></token> | 412 ]]></token> |
480 <xml name="params_plots"> | 413 <xml name="params_plots"> |
481 <expand macro="pl_var_names"/> | 414 <expand macro="pl_var_names"/> |
510 #silent $var_group_positions.append((int($s.start), int($s.end))) | 443 #silent $var_group_positions.append((int($s.start), int($s.end))) |
511 #silent $var_group_labels.append(str($s.label)) | 444 #silent $var_group_labels.append(str($s.label)) |
512 #end for | 445 #end for |
513 var_group_positions=$var_group_positions, | 446 var_group_positions=$var_group_positions, |
514 var_group_labels=$var_group_labels, | 447 var_group_labels=$var_group_labels, |
515 #else | |
516 var_group_positions=None, | |
517 var_group_labels=None, | |
518 #end if | 448 #end if |
519 #if $method.var_group_rotation | 449 #if $method.var_group_rotation |
520 var_group_rotation=$method.var_group_rotation, | 450 var_group_rotation=$method.var_group_rotation, |
521 #end if | 451 #end if |
522 #if $method.figsize.test == 'yes' | 452 #if $method.figsize.test == 'yes' |
727 alpha=$method.matplotlib_pyplot_scatter.alpha, | 657 alpha=$method.matplotlib_pyplot_scatter.alpha, |
728 #end if | 658 #end if |
729 linewidths=$method.matplotlib_pyplot_scatter.linewidths, | 659 linewidths=$method.matplotlib_pyplot_scatter.linewidths, |
730 edgecolors='$method.matplotlib_pyplot_scatter.edgecolors' | 660 edgecolors='$method.matplotlib_pyplot_scatter.edgecolors' |
731 ]]></token> | 661 ]]></token> |
732 <xml name="section_violin_plots"> | 662 <xml name="conditional_stripplot"> |
733 <section name="violin_plot" title="Violin plot attributes"> | 663 <conditional name="stripplot"> |
734 <conditional name="stripplot"> | 664 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help=""> |
735 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help=""> | 665 <option value="True">Yes</option> |
736 <option value="True">Yes</option> | 666 <option value="False">No</option> |
737 <option value="False">No</option> | |
738 </param> | |
739 <when value="True"> | |
740 <conditional name="jitter"> | |
741 <param argument="jitter" type="select" label="Add a jitter to the stripplot" help=""> | |
742 <option value="True">Yes</option> | |
743 <option value="False">No</option> | |
744 </param> | |
745 <when value="True"> | |
746 <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/> | |
747 </when> | |
748 <when value="False"/> | |
749 </conditional> | |
750 </when> | |
751 <when value="False"/> | |
752 </conditional> | |
753 <conditional name="multi_panel"> | |
754 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided"> | |
755 <option value="True">Yes</option> | |
756 <option value="False" selected="true">No</option> | |
757 </param> | |
758 <when value="True"> | |
759 <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/> | |
760 <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/> | |
761 </when> | |
762 <when value="False"/> | |
763 </conditional> | |
764 <param argument="scale" type="select" label="Method used to scale the width of each violin"> | |
765 <option value="area">area: each violin will have the same area</option> | |
766 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option> | |
767 <option value="width" selected="true">width: each violin will have the same width</option> | |
768 </param> | 667 </param> |
769 </section> | 668 <when value="True"> |
669 <conditional name="jitter"> | |
670 <param argument="jitter" type="select" label="Add a jitter to the stripplot" help=""> | |
671 <option value="True">Yes</option> | |
672 <option value="False">No</option> | |
673 </param> | |
674 <when value="True"> | |
675 <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/> | |
676 </when> | |
677 <when value="False"/> | |
678 </conditional> | |
679 </when> | |
680 <when value="False"/> | |
681 </conditional> | |
682 </xml> | |
683 <token name="@CMD_conditional_stripplot@"><![CDATA[ | |
684 stripplot=$method.violin_plot.stripplot.stripplot, | |
685 #if $method.violin_plot.stripplot.stripplot == "True" | |
686 jitter=$method.violin_plot.stripplot.jitter.jitter, | |
687 #if $method.violin_plot.stripplot.jitter.jitter == "True" | |
688 size=$method.violin_plot.stripplot.jitter.size, | |
689 #end if | |
690 #end if | |
691 ]]></token> | |
692 <xml name="param_scale"> | |
693 <param argument="scale" type="select" label="Method used to scale the width of each violin"> | |
694 <option value="area">area: each violin will have the same area</option> | |
695 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option> | |
696 <option value="width" selected="true">width: each violin will have the same width</option> | |
697 </param> | |
770 </xml> | 698 </xml> |
771 <token name="@CMD_params_violin_plots@"><![CDATA[ | 699 <token name="@CMD_params_violin_plots@"><![CDATA[ |
772 stripplot=$method.violin_plot.stripplot.stripplot, | 700 stripplot=$method.violin_plot.stripplot.stripplot, |
773 #if $method.violin_plot.stripplot.stripplot == "True" | 701 #if $method.violin_plot.stripplot.stripplot == "True" |
774 jitter=$method.violin_plot.stripplot.jitter.jitter, | 702 jitter=$method.violin_plot.stripplot.jitter.jitter, |
775 #if $method.violin_plot.stripplot.jitter.jitter == "True" | 703 #if $method.violin_plot.stripplot.jitter.jitter == "True" |
776 size=$method.violin_plot.stripplot.jitter.size, | 704 size=$method.violin_plot.stripplot.jitter.size, |
777 #end if | 705 #end if |
778 #end if | 706 #end if |
779 multi_panel=$method.violin_plot.multi_panel.multi_panel, | 707 multi_panel=$method.violin_plot.multi_panel.multi_panel, |
780 #if $method.multi_panel.violin_plot.multi_panel == "True" and $method.violin_plot.multi_panel.width and $method.violin_plot.multi_panel.height | 708 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != '' |
781 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) | 709 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) |
782 #end if | 710 #end if |
783 scale='$method.violin_plot.scale', | 711 scale='$method.violin_plot.scale', |
784 ]]></token> | 712 ]]></token> |
785 <xml name="seaborn_violinplot"> | 713 <xml name="seaborn_violinplot"> |
811 color='$method.seaborn_violinplot.color', | 739 color='$method.seaborn_violinplot.color', |
812 palette='$method.seaborn_violinplot.palette', | 740 palette='$method.seaborn_violinplot.palette', |
813 saturation=$method.seaborn_violinplot.saturation, | 741 saturation=$method.seaborn_violinplot.saturation, |
814 ]]></token> | 742 ]]></token> |
815 <xml name="param_color"> | 743 <xml name="param_color"> |
816 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes`" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/> | 744 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/> |
817 </xml> | 745 </xml> |
818 <token name="@CMD_param_color@"><![CDATA[ | 746 <token name="@CMD_param_color@"><![CDATA[ |
819 #if str($method.color) != '' | 747 #if str($method.color) != '' |
820 #set $color = ([x.strip() for x in str($method.color).split(',')]) | 748 #set $color = ([x.strip() for x in str($method.color).split(',')]) |
821 color=$color, | 749 color=$color, |
822 #else | |
823 color=None, | |
824 #end if | 750 #end if |
825 ]]></token> | 751 ]]></token> |
826 <xml name="pl_groups"> | 752 <xml name="pl_groups"> |
827 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/> | 753 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/> |
828 </xml> | 754 </xml> |
829 <token name="@CMD_params_pl_groups@"><![CDATA[ | 755 <token name="@CMD_params_pl_groups@"><![CDATA[ |
830 #if str($method.groups) != '' | 756 #if str($method.groups) != '' |
831 #set $groups=([x.strip() for x in str($method.groups).split(',')]) | 757 #set $groups=([x.strip() for x in str($method.groups).split(',')]) |
832 groups=$groups, | 758 groups=$groups, |
833 #else | |
834 groups=None, | |
835 #end if | 759 #end if |
836 ]]></token> | 760 ]]></token> |
837 <xml name="pl_components"> | 761 <xml name="pl_components"> |
838 <repeat name="components" title="Component"> | 762 <repeat name="components" title="Component"> |
839 <param argument="axis1" type="text" value="1" label="Axis 1" help=""/> | 763 <param argument="axis1" type="text" value="1" label="Axis 1" help=""/> |
845 #set $components=[] | 769 #set $components=[] |
846 #for $i, $s in enumerate($method.plot.components) | 770 #for $i, $s in enumerate($method.plot.components) |
847 #silent $components.append(str($s.axis1) + ',' + str($s.axis2)) | 771 #silent $components.append(str($s.axis1) + ',' + str($s.axis2)) |
848 #end for | 772 #end for |
849 components=$components, | 773 components=$components, |
850 #else | |
851 components=None, | |
852 #end if | 774 #end if |
853 ]]> | 775 ]]> |
854 </token> | 776 </token> |
855 <xml name="param_projection"> | 777 <xml name="param_projection"> |
856 <param argument="projection" type="select" label="Projection of plot" help=""> | 778 <param argument="projection" type="select" label="Projection of plot" help=""> |
875 <option value="upper center">upper center</option> | 797 <option value="upper center">upper center</option> |
876 <option value="center">center</option> | 798 <option value="center">center</option> |
877 </param> | 799 </param> |
878 </xml> | 800 </xml> |
879 <xml name="param_legend_fontsize"> | 801 <xml name="param_legend_fontsize"> |
880 <param argument="legend_fontsize" type="integer" min="0" value="1" label="Legend font size" help=""/> | 802 <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/> |
881 </xml> | 803 </xml> |
882 <xml name="param_legend_fontweight"> | 804 <xml name="param_legend_fontweight"> |
883 <param argument="legend_fontweight" type="select" label="Legend font weight" help=""> | 805 <param argument="legend_fontweight" type="select" label="Legend font weight" help=""> |
884 <option value="light">light</option> | 806 <option value="light">light</option> |
885 <option value="normal" selected="true">normal</option> | 807 <option value="normal" selected="true">normal</option> |
908 </xml> | 830 </xml> |
909 <xml name="param_left_margin"> | 831 <xml name="param_left_margin"> |
910 <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/> | 832 <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/> |
911 </xml> | 833 </xml> |
912 <xml name="param_size"> | 834 <xml name="param_size"> |
913 <param argument="size" type="float" value="1" label="Point size" help=""/> | 835 <param argument="size" type="float" optional="true" value="" label="Point size" help=""/> |
914 </xml> | 836 </xml> |
915 <xml name="param_title"> | 837 <xml name="param_title"> |
916 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/> | 838 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/> |
917 </xml> | 839 </xml> |
918 <xml name="param_sort_order"> | 840 <xml name="param_sort_order"> |
935 <param argument="edges" type="select" label="Show edges?"> | 857 <param argument="edges" type="select" label="Show edges?"> |
936 <option value="True">Yes</option> | 858 <option value="True">Yes</option> |
937 <option value="False" selected="true">No</option> | 859 <option value="False" selected="true">No</option> |
938 </param> | 860 </param> |
939 <when value="True"> | 861 <when value="True"> |
940 <param name="edges_width" type="float" min="0" value="0.1" label="Width of edges"/> | 862 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/> |
941 <param name="edges_color" type="select" label="Color of edges"> | 863 <param argument="edges_color" type="select" label="Color of edges"> |
942 <expand macro="matplotlib_color"/> | 864 <expand macro="matplotlib_color"/> |
943 </param> | 865 </param> |
944 </when> | 866 </when> |
945 <when value="False"/> | 867 <when value="False"/> |
946 </conditional> | 868 </conditional> |
954 edges=False, | 876 edges=False, |
955 #end if | 877 #end if |
956 ]]> | 878 ]]> |
957 </token> | 879 </token> |
958 <xml name="param_arrows"> | 880 <xml name="param_arrows"> |
959 <param name="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/> | 881 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/> |
960 </xml> | 882 </xml> |
961 <xml name="param_cmap"> | 883 <xml name="param_cmap"> |
962 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> | 884 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> |
963 <expand macro="matplotlib_pyplot_colormap"/> | 885 <expand macro="matplotlib_pyplot_colormap"/> |
964 </param> | 886 </param> |
980 </section> | 902 </section> |
981 </xml> | 903 </xml> |
982 <token name="@CMD_pl_attribute_section@"><![CDATA[ | 904 <token name="@CMD_pl_attribute_section@"><![CDATA[ |
983 projection='$method.plot.projection', | 905 projection='$method.plot.projection', |
984 legend_loc='$method.plot.legend_loc', | 906 legend_loc='$method.plot.legend_loc', |
907 #if str($method.plot.legend_fontsize) != '' | |
985 legend_fontsize=$method.plot.legend_fontsize, | 908 legend_fontsize=$method.plot.legend_fontsize, |
909 #end if | |
986 legend_fontweight='$method.plot.legend_fontweight', | 910 legend_fontweight='$method.plot.legend_fontweight', |
911 #if str($method.plot.size) != '' | |
987 size=$method.plot.size, | 912 size=$method.plot.size, |
913 #end if | |
988 palette='$method.plot.palette', | 914 palette='$method.plot.palette', |
989 frameon=$method.plot.frameon, | 915 frameon=$method.plot.frameon, |
990 ncols=$method.plot.ncols, | 916 ncols=$method.plot.ncols, |
991 wspace=$method.plot.wspace, | 917 wspace=$method.plot.wspace, |
992 hspace=$method.plot.hspace, | 918 hspace=$method.plot.hspace, |
993 #if $method.plot.title | 919 #if $method.plot.title |
994 title='$method.plot.title', | 920 title='$method.plot.title', |
995 #end if | 921 #end if |
996 ]]> | 922 ]]> |
997 </token> | 923 </token> |
924 <xml name="options_layout"> | |
925 <option value="fa">fa: ForceAtlas2</option> | |
926 <option value="fr">fr: Fruchterman-Reingold</option> | |
927 <option value="grid_fr">grid_fr: Grid Fruchterman Reingold, faster than "fr"</option> | |
928 <option value="kk">kk: Kamadi Kawai’, slower than "fr"</option> | |
929 <option value="drl">drl: Distributed Recursive Layout, pretty fast</option> | |
930 <option value="rt">rt: Reingold Tilford tree layout</option> | |
931 <option value="eq_tree">eq_tree: Equally spaced tree</option> | |
932 </xml> | |
933 <xml name="param_layout"> | |
934 <param argument="layout" type="select" label="Plotting layout" help=""> | |
935 <expand macro="options_layout"/> | |
936 </param> | |
937 </xml> | |
938 <xml name="param_root"> | |
939 <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is `None` or an empty list, the root vertices are automatically calculated based on topological sorting."/> | |
940 </xml> | |
941 <xml name="param_random_state"> | |
942 <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If `None`, the initial state is not reproducible."/> | |
943 </xml> | |
998 <xml name="inputs_paga"> | 944 <xml name="inputs_paga"> |
999 <param argument="threshold" type="float" min="0" value="0.01" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/> | 945 <param argument="threshold" type="float" min="0" value="0.01" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/> |
1000 <expand macro="pl_groups"/> | 946 <expand macro="pl_groups"/> |
1001 <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."/> | 947 <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."/> |
1002 <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/> | 948 <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/> |
1003 <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which `tl.paga` has been computed."/> | 949 <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which `tl.paga` has been computed."/> |
1004 <param argument="layout" type="select" value="" label="Plotting layout" help=""> | 950 <expand macro="param_layout"/> |
1005 <option value="fa">fa: ForceAtlas2</option> | |
1006 <option value="fr">fr: Fruchterman-Reingold</option> | |
1007 <option value="fr">rt: stands for Reingold Tilford</option> | |
1008 <option value="fr">eq_tree: equally spaced tree</option> | |
1009 </param> | |
1010 <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/> | 951 <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/> |
1011 <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If `None`, the initial state is not reproducible."/> | 952 <expand macro="param_random_state"/> |
1012 <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is `None` or an empty list, the root vertices are automatically calculated based on topological sorting."/> | 953 <expand macro="param_root"/> |
1013 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/> | 954 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/> |
1014 <param argument="solid_edges" type="text" value="paga_connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for `.uns['paga']`"/> | 955 <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga"/> |
1015 <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for `.uns['paga']`. If not set, no dashed edges are drawn."/> | 956 <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn."/> |
1016 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/> | 957 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/> |
1017 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/> | 958 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/> |
1018 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/> | 959 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/> |
1019 <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/> | 960 <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/> |
1020 <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/> | 961 <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/> |
1029 <token name="@CMD_params_pl_paga@"><![CDATA[ | 970 <token name="@CMD_params_pl_paga@"><![CDATA[ |
1030 threshold=$method.threshold, | 971 threshold=$method.threshold, |
1031 #if str($method.groups) != '' | 972 #if str($method.groups) != '' |
1032 #set $groups=([x.strip() for x in str($method.groups).split(',')]) | 973 #set $groups=([x.strip() for x in str($method.groups).split(',')]) |
1033 groups=$groups, | 974 groups=$groups, |
1034 #else | 975 #end if |
1035 groups=None, | 976 #if str($method.color) != '' |
1036 #end if | 977 #set $color=([x.strip() for x in str($method.color).split(',')]) |
1037 color='$method.color', | 978 color=$color, |
979 #end if | |
1038 #if $method.pos | 980 #if $method.pos |
1039 pos=np.fromfile($method.pos, dtype=dt), | 981 pos=np.fromfile($method.pos, dtype=dt), |
1040 #end if | 982 #end if |
1041 #if str($method.labels) != '' | 983 #if str($method.labels) != '' |
1042 #set $labels=([x.strip() for x in str($method.labels).split(',')]) | 984 #set $labels=([x.strip() for x in str($method.labels).split(',')]) |
1079 ]]> | 1021 ]]> |
1080 </token> | 1022 </token> |
1081 <xml name="param_swap_axes"> | 1023 <xml name="param_swap_axes"> |
1082 <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains `var_names` (e.g. genes) and the y axis the `groupby` categories (if any). By setting `swap_axes` then x are the `groupby` categories and y the `var_names`."/> | 1024 <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains `var_names` (e.g. genes) and the y axis the `groupby` categories (if any). By setting `swap_axes` then x are the `groupby` categories and y the `var_names`."/> |
1083 </xml> | 1025 </xml> |
1026 <xml name="gene_symbols"> | |
1027 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in `.var` that stores gene symbols"/> | |
1028 </xml> | |
1029 <xml name="n_genes"> | |
1030 <param argument="n_genes" type="integer" min="0" value="20" label="Number of genes to show" help=""/> | |
1031 </xml> | |
1084 </macros> | 1032 </macros> |