| Previous changeset 11:7dd841a32245 (2022-10-01) Next changeset 13:360df4999907 (2023-03-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 26f4478d873b339c5a1eccf18df68700a145a404 |
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modified:
macros.xml pyGenomeTracks.xml test-data/bigwig_multiple.png test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/master_fasta.png test-data/master_scale_bar_startend.png test-data/test1.ini test-data/test9.ini test-data/test_TADs_bdgm.png test-data/test_alpha.png test-data/test_alpha_dec.png test-data/test_arcs_use_middle.png test-data/test_arrowhead_zoom.png test-data/test_gtf_bed4.png test-data/test_gtf_flybase_param.png test-data/test_link.png test-data/test_link2.png test-data/test_log.png test-data/test_log_grid.png test-data/test_maf.png test-data/test_matrix_square.png test-data/test_middle_triangle.png test-data/test_narrowPeak.png test-data/test_operation.png test-data/test_scale_bar.png test-data/test_tssarrow.png test-data/test_ucsc_param.png test-data/test_vhighlight.png |
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added:
static/images/demo.png static/images/demo2.png test-data/dm3_genes_end.bed |
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removed:
static/images/pyGenomeTracks.png |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 macros.xml --- a/macros.xml Sat Oct 01 08:43:22 2022 +0000 +++ b/macros.xml Wed Jan 25 15:33:12 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">3.7</token> + <token name="@TOOL_VERSION@">3.8</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 pyGenomeTracks.xml --- a/pyGenomeTracks.xml Sat Oct 01 08:43:22 2022 +0000 +++ b/pyGenomeTracks.xml Wed Jan 25 15:33:12 2023 +0000 |
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| @@ -581,6 +581,10 @@ [vlines_$counter] file = $track.track_file_style_conditional.track_input_bed_single line_width = $track.track_file_style_conditional.line_width +line_style = $track.track_file_style_conditional.line_style +color = $track.track_file_style_conditional.color +alpha = $track.track_file_style_conditional.alpha +zorder = $track.track_file_style_conditional.zorder type = vlines #end if @@ -588,8 +592,10 @@ #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option": [vhighlight_$counter] file = $track.track_file_style_conditional.track_input_bed_single +line_width = $track.track_file_style_conditional.line_width color = $track.track_file_style_conditional.color alpha = $track.track_file_style_conditional.alpha +border_color = $track.track_file_style_conditional.border_color type = vhighlight #end if @@ -1185,11 +1191,29 @@ <when value="vlines_track_option"> <expand macro="track_input_bed_single_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines"/> + <param name="line_style" type="select" label="Line Style"> + <option value="dashed">Dashed</option> + <option value="solid">Solid</option> + <option value="dotted">Dotted</option> + <option value="dashdot">Dashdot</option> + </param> + <param name="color" type="color" value="black" label="color of the vline"/> + <param name="alpha" type="float" value="0.7" min="0" max="1" label="transparency (alpha) of the vline"/> + <param name="zorder" type="select" label="Plot the vline above or behind other tracks"> + <option value="100">above</option> + <option value="-100">behind</option> + </param> </when> <when value="vhighlight_track_option"> <expand macro="track_input_bed_single_macro" /> <param name="color" type="color" value="yellow" label="color of the highlight"/> <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/> + <param name="line_width" type="float" min="0" value="0.5" label="width of the edge of the highlight" /> + <param name="border_color" type="color" value="yellow" label="color of the edge of the highlight"/> + <param name="zorder" type="select" label="Plot the highlight above or behind other tracks"> + <option value="-100">behind</option> + <option value="100">above</option> + </param> </when> <when value="hlines_track_option"> <expand macro="plot_title" /> @@ -2169,6 +2193,19 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="vlines_track_option" /> <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> + <param name="line_width" value="2"/> + <param name="zorder" value="100"/> + <param name="color" value="red"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="vlines_track_option" /> + <param name="track_input_bed_single" value="dm3_genes_end.bed" ftype="bed" /> + <param name="line_width" value="5"/> + <param name="zorder" value="-100"/> + <param name="color" value="blue"/> + <param name="line_style" value="solid"/> </conditional> </repeat> <param name="image_file_format" value="png" /> @@ -3336,16 +3373,13 @@ Output ------ -**pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) -may also contains Hi-C data. The plot is composed of tracks that need to be specified. -Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. -TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: -TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, -principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. -Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. +Here are two example plots with the different tracks you can use (on the right, you have the vlines and vhighlight which have been used): -.. image:: $PATH_TO_IMAGES/pyGenomeTracks.png - :width: 70 % +.. image:: static/images/demo.png + :width: 45 % +.. image:: static/images/demo2.png + :width: 45 % + _________________ |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 static/images/demo.png |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/bigwig_multiple.png |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/dm3_genes_end.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dm3_genes_end.bed Wed Jan 25 15:33:12 2023 +0000 |
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| @@ -0,0 +1,7 @@ +chrX 3130718 3130719 CG14265_end +chrX 3134603 3134604 ng2_end +chrX 3136116 3136117 ng3_end +chrX 3136966 3136967 ng1_end +chrX 3138252 3138253 ng4_end +chrX 3143321 3143322 Pig1_end +chrX 3145072 3145073 Sgs4_end |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/master_TADs_BW_plot.png |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/master_TADs_plot.png |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test1.ini --- a/test-data/test1.ini Sat Oct 01 08:43:22 2022 +0000 +++ b/test-data/test1.ini Wed Jan 25 15:33:12 2023 +0000 |
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| @@ -1,6 +1,6 @@ [x-axis] where = top -[hic_section_0_0] +[hic_section_1_0] file = test-data/Li_et_al_2015.h5 file_type = hic_matrix title = Kc DpnII (Li et al. 2015) @@ -9,7 +9,7 @@ transform = log1p scale_factor = 1.0 rasterize = true -[tads_0_0] +[tads_1_0] file = test-data/domains.bed file_type = domains border_color = black @@ -17,7 +17,7 @@ overlay_previous = share-y [spacer] height = 0.05 -[chrom states_2] +[chrom states_3] file = test-data/tad_classification.bed title = TAD state color = bed_rgb @@ -26,17 +26,15 @@ height = 0.5 line_width = 0.5 file_type = bed -[bedgraph_matrix_3] +[bedgraph_matrix_4] file = test-data/tad_score.gz title = TAD separation score (Ramirez et al.) height = 10.0 +type = matrix file_type = bedgraph_matrix -show_data_range = false -plot_horizontal_lines = false -pos_score_in_bin = center [spacer] height = 1.0 -[bedgraph_5] +[bedgraph_6] file = test-data/bedgraph_chrx_2e6_5e6.bg title = bedgraph color = blue @@ -48,7 +46,7 @@ file_type = bedgraph type = fill overlay_previous = no -[bigwig_6] +[bigwig_7] file = test-data/bigwig_chrx_2e6_5e6.bw title = rep 1 test fill color = blue @@ -60,7 +58,7 @@ show_data_range = false file_type = bigwig overlay_previous = no -[bigwig_7] +[bigwig_8] file = test-data/bigwig_chrx_2e6_5e6.bw title = rep 1 test line color = red @@ -72,7 +70,7 @@ show_data_range = false file_type = bigwig overlay_previous = no -[bigwig_8] +[bigwig_9] file = test-data/bigwig_chrx_2e6_5e6.bw title = rep 1 test lw=0.2 color = red @@ -84,7 +82,7 @@ show_data_range = false file_type = bigwig overlay_previous = no -[bigwig_9] +[bigwig_10] file = test-data/bigwig_chrx_2e6_5e6.bw title = rep 1 test point:0.5 color = black @@ -98,7 +96,7 @@ overlay_previous = no [spacer] height = 0.5 -[genes_11_0] +[genes_12_0] file = test-data/dm3_genes.bed.gz title = genes color = #000000 @@ -109,8 +107,8 @@ display = stacked height = 5.0 labels = true +fontsize = 10 file_type = bed -fontsize = 10 global_max_row = false max_labels = 60 line_width = 0.5 @@ -118,7 +116,7 @@ overlay_previous = no [spacer] height = 1.0 -[genes_13_0] +[genes_14_0] file = test-data/dm3_genes.bed.gz title = max num rows 3 color = #000000 @@ -139,7 +137,7 @@ overlay_previous = no [spacer] height = 1.0 -[genes_15_0] +[genes_16_0] file = test-data/dm3_genes.bed6.gz title = bed6 global max row color = #000000 @@ -157,6 +155,6 @@ line_width = 0.5 arrowhead_included = false overlay_previous = no -[vlines_16] +[vlines_17] file = test-data/domains.bed -type = vlines \ No newline at end of file +type = vlines |
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| diff -r 7dd841a32245 -r 14e7c35f3d00 test-data/test9.ini --- a/test-data/test9.ini Sat Oct 01 08:43:22 2022 +0000 +++ b/test-data/test9.ini Wed Jan 25 15:33:12 2023 +0000 |
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| @@ -97,5 +97,14 @@ height = 1.0 [vlines_5] file = dm3_subset_BDGP5.78_asbed4.bed.gz -line_width = 0.5 -type = vlines \ No newline at end of file +line_width = 2 +zorder = 100 +color = red +type = vlines +[vlines_6] +file = dm3_genes_end.bed +line_width = 5 +zorder = -100 +color = blue +line_style = solid +type = vlines |
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