# HG changeset patch # User iuc # Date 1711558391 0 # Node ID 76c2567165fa150e2c2d941ecd3085b9b3b11e34 # Parent b6faa1142f8375444a256b7721c87f4c18854e4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d diff -r b6faa1142f83 -r 76c2567165fa macros.xml --- a/macros.xml Mon Mar 04 19:56:22 2024 +0000 +++ b/macros.xml Wed Mar 27 16:53:11 2024 +0000 @@ -1,5 +1,5 @@ - 0.2.2 + 0.2.4 1 pca @@ -12,6 +12,12 @@ + + + + + + @@ -166,6 +172,7 @@ + @@ -638,14 +645,23 @@ #if $metadata_path: ln -s '$metadata_path' data/metadata.csv && #end if + + #set conditions_MDV_comparison = {} - #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson' #set timepoints_MDV_comparison = {} - #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson' #set conditions_metabolite_time_profiles = {} - #silent $conditions_metabolite_time_profiles['abundances']='pearson' - #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' + #if str( $stat_test ) == "pearson": + #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson' + #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson' + #silent $conditions_metabolite_time_profiles['abundances']='pearson' + #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' + #else + #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman' + #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman' + #silent $conditions_metabolite_time_profiles['abundances']='spearman' + #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman' + #end if #set $impute_values = {} #if str( $data_input.data_input_selector ) == "abundance": #if $data_input.abundance_file: diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--cell--label-n_pc.svg --- a/test-data/abundances--T0--cell--label-n_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T0--cell--label-n_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.244122 + 2024-03-26T10:28:20.939491 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#pab131b2223)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#pab131b2223)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -203,7 +200,7 @@ - + @@ -419,12 +416,12 @@ - - + @@ -472,7 +469,7 @@ - + @@ -486,7 +483,7 @@ - + @@ -500,7 +497,7 @@ - + @@ -513,7 +510,7 @@ - + @@ -526,7 +523,7 @@ - + @@ -539,7 +536,7 @@ - + @@ -586,7 +583,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#pab131b2223)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#pab131b2223)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#pab131b2223)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#pab131b2223)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -839,22 +842,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -966,9 +969,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1080,7 +1084,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--cell--label-y_pc.svg --- a/test-data/abundances--T0--cell--label-y_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T0--cell--label-y_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.195225 + 2024-03-26T10:28:20.904175 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#p4516990cc5)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#p4516990cc5)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -203,7 +200,7 @@ - + @@ -419,12 +416,12 @@ - - + @@ -472,7 +469,7 @@ - + @@ -486,7 +483,7 @@ - + @@ -500,7 +497,7 @@ - + @@ -513,7 +510,7 @@ - + @@ -526,7 +523,7 @@ - + @@ -539,7 +536,7 @@ - + @@ -586,7 +583,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#p4516990cc5)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p4516990cc5)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p4516990cc5)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p4516990cc5)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + @@ -870,9 +872,10 @@ z " style="fill: #ffffff; opacity: 0.8; stroke: #cccccc; stroke-linejoin: miter"/> + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -995,22 +998,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1064,9 +1067,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1165,7 +1169,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--cell_pc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--cell_pc.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +PC1 PC2 PC3 PC4 name_to_plot condition timepoint timenum compartment original_name +-4.612574 -2.881005 -0.432059 0.0 Ctrl_cell_T0-1 Control T0 0 cell MCF001089_TD01 +-3.303276 3.622393 -0.061907 0.0 Ctrl_cell_T0-2 Control T0 0 cell MCF001089_TD02 +1.95919 -0.773766 1.28576 0.0 L-Cyc_cell_T0-1 L-Cycloserine T0 0 cell MCF001089_TD19 +5.95666 0.032379 -0.791794 0.0 L-Cyc_cell_T0-2 L-Cycloserine T0 0 cell MCF001089_TD20 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--cell_var.svg --- a/test-data/abundances--T0--cell_var.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T0--cell_var.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.157274 + 2024-03-26T10:28:20.870816 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -43,7 +43,7 @@ L 137.952 54.144 L 66.528 54.144 z -" clip-path="url(#pc312d5c87f)" style="fill: #679698"/> +" clip-path="url(#p596071d219)" style="fill: #679698"/> +" clip-path="url(#p596071d219)" style="fill: #679698"/> +" clip-path="url(#p596071d219)" style="fill: #679698"/> +" clip-path="url(#p596071d219)" style="fill: #679698"/> - - + @@ -151,7 +151,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -241,7 +241,7 @@ - + @@ -286,12 +286,12 @@ - - + @@ -327,7 +327,7 @@ - + @@ -341,7 +341,7 @@ - + @@ -355,7 +355,7 @@ - + @@ -369,7 +369,7 @@ - + @@ -383,7 +383,7 @@ - + @@ -424,7 +424,7 @@ - + @@ -470,7 +470,7 @@ - + @@ -857,16 +857,16 @@ - + - + - + - + + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--cell_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--cell_var.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +Explained Variance % PC +74.487179 PC1 +22.939254 PC2 +2.573566 PC3 +0.0 PC4 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--med--label-n_pc.svg --- a/test-data/abundances--T0--med--label-n_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T0--med--label-n_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.654753 + 2024-03-26T10:28:21.250564 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#p6931c9dd59)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#p6931c9dd59)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -458,12 +455,12 @@ - - + @@ -477,7 +474,7 @@ - + @@ -491,7 +488,7 @@ - + @@ -504,7 +501,7 @@ - + @@ -517,7 +514,7 @@ - + @@ -530,7 +527,7 @@ - + @@ -611,7 +608,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#p6931c9dd59)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p6931c9dd59)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p6931c9dd59)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p6931c9dd59)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -864,22 +867,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -991,9 +994,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1105,7 +1109,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--med--label-y_pc.svg --- a/test-data/abundances--T0--med--label-y_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T0--med--label-y_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.612723 + 2024-03-26T10:28:21.216178 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#pc58fddc43c)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#pc58fddc43c)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -458,12 +455,12 @@ - - + @@ -477,7 +474,7 @@ - + @@ -491,7 +488,7 @@ - + @@ -504,7 +501,7 @@ - + @@ -517,7 +514,7 @@ - + @@ -530,7 +527,7 @@ - + @@ -611,7 +608,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#pc58fddc43c)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#pc58fddc43c)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#pc58fddc43c)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#pc58fddc43c)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + @@ -947,9 +949,10 @@ z " style="fill: #ffffff; opacity: 0.8; stroke: #cccccc; stroke-linejoin: miter"/> + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1046,22 +1049,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1115,9 +1118,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1186,7 +1190,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--med_pc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--med_pc.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +PC1 PC2 PC3 PC4 name_to_plot condition timepoint timenum compartment original_name +-3.647549 -2.371648 -1.342906 0.0 Ctrl_med_T0-1 Control T0 0 med MCF001089_TD37 +-2.455848 3.273883 0.058928 0.0 Ctrl_med_T0-2 Control T0 0 med MCF001089_TD38 +4.873764 0.136899 -1.737705 0.0 L-Cyc_med_T0-1 L-Cycloserine T0 0 med MCF001089_TD55 +1.229634 -1.039134 3.021683 0.0 L-Cyc_med_T0-2 L-Cycloserine T0 0 med MCF001089_TD56 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--med_var.svg --- a/test-data/abundances--T0--med_var.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T0--med_var.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.575574 + 2024-03-26T10:28:21.184677 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -43,7 +43,7 @@ L 137.952 54.144 L 66.528 54.144 z -" clip-path="url(#p66313797f2)" style="fill: #679698"/> +" clip-path="url(#pc7004c9502)" style="fill: #679698"/> +" clip-path="url(#pc7004c9502)" style="fill: #679698"/> +" clip-path="url(#pc7004c9502)" style="fill: #679698"/> +" clip-path="url(#pc7004c9502)" style="fill: #679698"/> - - + @@ -151,7 +151,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -241,7 +241,7 @@ - + @@ -286,12 +286,12 @@ - - + @@ -327,7 +327,7 @@ - + @@ -341,7 +341,7 @@ - + @@ -355,7 +355,7 @@ - + @@ -369,7 +369,7 @@ - + @@ -383,7 +383,7 @@ - + @@ -424,7 +424,7 @@ - + @@ -831,16 +831,16 @@ - + - + - + - + + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T0--med_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--med_var.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +Explained Variance % PC +58.686028 PC1 +22.949429 PC2 +18.364542 PC3 +0.0 PC4 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--cell--label-n_pc.svg --- a/test-data/abundances--T2h--cell--label-n_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T2h--cell--label-n_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.360072 + 2024-03-26T10:28:21.040188 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#p1f309fd952)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#p1f309fd952)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -203,7 +200,7 @@ - + @@ -418,12 +415,12 @@ - - + @@ -466,7 +463,7 @@ - + @@ -482,7 +479,7 @@ - + @@ -498,7 +495,7 @@ - + @@ -513,7 +510,7 @@ - + @@ -528,7 +525,7 @@ - + @@ -543,7 +540,7 @@ - + @@ -558,7 +555,7 @@ - + @@ -606,7 +603,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#p1f309fd952)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p1f309fd952)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p1f309fd952)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p1f309fd952)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -859,22 +862,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -986,9 +989,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1120,7 +1124,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--cell--label-y_pc.svg --- a/test-data/abundances--T2h--cell--label-y_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T2h--cell--label-y_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.313549 + 2024-03-26T10:28:21.003691 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#p23949f7454)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#p23949f7454)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -203,7 +200,7 @@ - + @@ -418,12 +415,12 @@ - - + @@ -466,7 +463,7 @@ - + @@ -482,7 +479,7 @@ - + @@ -498,7 +495,7 @@ - + @@ -513,7 +510,7 @@ - + @@ -528,7 +525,7 @@ - + @@ -543,7 +540,7 @@ - + @@ -558,7 +555,7 @@ - + @@ -606,7 +603,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#p23949f7454)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p23949f7454)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p23949f7454)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p23949f7454)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + @@ -913,9 +915,10 @@ z " style="fill: #ffffff; opacity: 0.8; stroke: #cccccc; stroke-linejoin: miter"/> + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1038,22 +1041,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1107,9 +1110,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1209,7 +1213,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--cell_pc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T2h--cell_pc.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +PC1 PC2 PC3 PC4 name_to_plot condition timepoint timenum compartment original_name +3.418013 2.018827 -0.624963 0.0 Ctrl_cell_T2h-1 Control T2h 2 cell MCF001089_TD07 +-5.121119 -1.029264 -0.970952 0.0 Ctrl_cell_T2h-2 Control T2h 2 cell MCF001089_TD08 +5.604413 -1.686558 0.356619 0.0 L-Cyc_cell_T2h-1 L-Cycloserine T2h 2 cell MCF001089_TD25 +-3.901307 0.696996 1.239296 0.0 L-Cyc_cell_T2h-2 L-Cycloserine T2h 2 cell MCF001089_TD26 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--cell_var.svg --- a/test-data/abundances--T2h--cell_var.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T2h--cell_var.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.278168 + 2024-03-26T10:28:20.971900 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -43,7 +43,7 @@ L 137.952 54.144 L 66.528 54.144 z -" clip-path="url(#p5f41492c3f)" style="fill: #679698"/> +" clip-path="url(#p034a823787)" style="fill: #679698"/> +" clip-path="url(#p034a823787)" style="fill: #679698"/> +" clip-path="url(#p034a823787)" style="fill: #679698"/> +" clip-path="url(#p034a823787)" style="fill: #679698"/> - - + @@ -151,7 +151,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -241,7 +241,7 @@ - + @@ -286,12 +286,12 @@ - - + @@ -327,7 +327,7 @@ - + @@ -341,7 +341,7 @@ - + @@ -355,7 +355,7 @@ - + @@ -401,7 +401,7 @@ - + @@ -817,16 +817,16 @@ - + - + - + - + + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--cell_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T2h--cell_var.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +Explained Variance % PC +88.060744 PC1 +8.81805 PC2 +3.121206 PC3 +0.0 PC4 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--med--label-n_pc.svg --- a/test-data/abundances--T2h--med--label-n_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T2h--med--label-n_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.767663 + 2024-03-26T10:28:21.346891 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#p85ff2a3843)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#p85ff2a3843)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -435,12 +432,12 @@ - - + @@ -454,7 +451,7 @@ - + @@ -468,7 +465,7 @@ - + @@ -481,7 +478,7 @@ - + @@ -494,7 +491,7 @@ - + @@ -541,7 +538,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#p85ff2a3843)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p85ff2a3843)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p85ff2a3843)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p85ff2a3843)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -794,22 +797,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -921,9 +924,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1055,7 +1059,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--med--label-y_pc.svg --- a/test-data/abundances--T2h--med--label-y_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T2h--med--label-y_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.725828 + 2024-03-26T10:28:21.313686 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,29 +37,26 @@ z " style="fill: #ffffff"/> - - - +" clip-path="url(#p313813b882)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#p313813b882)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -101,7 +98,7 @@ - + @@ -141,7 +138,7 @@ - + @@ -177,7 +174,7 @@ - + @@ -190,7 +187,7 @@ - + @@ -435,12 +432,12 @@ - - + @@ -454,7 +451,7 @@ - + @@ -468,7 +465,7 @@ - + @@ -481,7 +478,7 @@ - + @@ -494,7 +491,7 @@ - + @@ -541,7 +538,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#p313813b882)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p313813b882)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p313813b882)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p313813b882)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + @@ -900,9 +902,10 @@ z " style="fill: #ffffff; opacity: 0.8; stroke: #cccccc; stroke-linejoin: miter"/> + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -999,22 +1002,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1068,9 +1071,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1140,7 +1144,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--med_pc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T2h--med_pc.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +PC1 PC2 PC3 PC4 name_to_plot condition timepoint timenum compartment original_name +-3.78242 2.157774 0.512581 0.0 Ctrl_med_T2h-1 Control T2h 2 med MCF001089_TD43 +-3.977769 -1.955737 -0.734513 0.0 Ctrl_med_T2h-2 Control T2h 2 med MCF001089_TD44 +3.226932 -0.99365 1.522596 0.0 L-Cyc_med_T2h-1 L-Cycloserine T2h 2 med MCF001089_TD61 +4.533256 0.791612 -1.300663 0.0 L-Cyc_med_T2h-2 L-Cycloserine T2h 2 med MCF001089_TD62 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--med_var.svg --- a/test-data/abundances--T2h--med_var.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--T2h--med_var.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.687841 + 2024-03-26T10:28:21.282602 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -43,7 +43,7 @@ L 137.952 54.144 L 66.528 54.144 z -" clip-path="url(#pfc5496463b)" style="fill: #679698"/> +" clip-path="url(#p72c3dab1fe)" style="fill: #679698"/> +" clip-path="url(#p72c3dab1fe)" style="fill: #679698"/> +" clip-path="url(#p72c3dab1fe)" style="fill: #679698"/> +" clip-path="url(#p72c3dab1fe)" style="fill: #679698"/> - - + @@ -151,7 +151,7 @@ - + @@ -192,7 +192,7 @@ - + @@ -241,7 +241,7 @@ - + @@ -286,12 +286,12 @@ - - + @@ -327,7 +327,7 @@ - + @@ -341,7 +341,7 @@ - + @@ -355,7 +355,7 @@ - + @@ -369,7 +369,7 @@ - + @@ -383,7 +383,7 @@ - + @@ -424,7 +424,7 @@ - + @@ -470,7 +470,7 @@ - + @@ -496,7 +496,7 @@ - + @@ -912,16 +912,16 @@ - + - + - + - + + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--T2h--med_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T2h--med_var.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,5 @@ +Explained Variance % PC +80.38532 PC1 +13.282744 PC2 +6.331936 PC3 +0.0 PC4 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--cell--label-n_pc.svg --- a/test-data/abundances--cell--label-n_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--cell--label-n_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.121728 + 2024-03-26T10:28:20.809039 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,30 +37,26 @@ z " style="fill: #ffffff"/> - - - - +" clip-path="url(#ped65f9af6a)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> +" clip-path="url(#ped65f9af6a)" style="fill: none; stroke-dasharray: 5.55,2.4; stroke-dashoffset: 0; stroke: #808080; stroke-width: 1.5"/> - - + @@ -113,7 +109,7 @@ - + @@ -148,7 +144,7 @@ - + @@ -188,7 +184,7 @@ - + @@ -224,7 +220,7 @@ - + @@ -237,7 +233,7 @@ - + @@ -250,7 +246,7 @@ - + @@ -403,12 +399,12 @@ - - + @@ -456,7 +452,7 @@ - + @@ -470,7 +466,7 @@ - + @@ -484,7 +480,7 @@ - + @@ -497,7 +493,7 @@ - + @@ -510,7 +506,7 @@ - + @@ -523,7 +519,7 @@ - + @@ -597,7 +593,7 @@ L 414.72 41.472 " style="fill: none; stroke: #000000; stroke-width: 0.8; stroke-linejoin: miter; stroke-linecap: square"/> - + +" clip-path="url(#ped65f9af6a)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #1f77b4; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#ped65f9af6a)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -906,22 +909,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1033,9 +1036,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1143,25 +1147,25 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542; stroke-linejoin: miter"/> - + @@ -1197,7 +1201,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--cell--label-y_pc.svg --- a/test-data/abundances--cell--label-y_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--cell--label-y_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.068925 + 2024-03-26T10:28:20.766162 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,30 +37,26 @@ z " style="fill: #ffffff"/> - - - - +" clip-path="url(#p504d07b906)" style="fill: none; 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stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p504d07b906)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p504d07b906)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p504d07b906)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p504d07b906)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + @@ -1040,9 +1042,10 @@ z " style="fill: #ffffff; opacity: 0.8; stroke: #cccccc; stroke-linejoin: miter"/> + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1165,22 +1168,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1234,9 +1237,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1331,25 +1335,25 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542; stroke-linejoin: miter"/> - + @@ -1364,7 +1368,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--cell_pc.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--cell_pc.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,9 @@ +PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 name_to_plot condition timepoint timenum compartment original_name +6.08216 -0.21243 2.741629 -0.415911 -0.034854 -0.297123 0.029912 0.0 Ctrl_cell_T0-1 Control T0 0 cell MCF001089_TD01 +4.441447 -3.400088 -2.014018 -0.157591 -0.036533 0.034759 0.178162 0.0 Ctrl_cell_T0-2 Control T0 0 cell MCF001089_TD02 +-4.500212 -0.722539 -0.451432 -1.053058 0.388746 -0.337473 -0.380903 0.0 Ctrl_cell_T2h-1 Control T2h 2 cell MCF001089_TD07 +2.559191 3.507152 -1.423484 -0.413442 -0.773312 0.004868 -0.038496 0.0 Ctrl_cell_T2h-2 Control T2h 2 cell MCF001089_TD08 +-0.401209 -0.824396 0.821053 0.46477 -0.229954 0.808554 -0.295096 0.0 L-Cyc_cell_T0-1 L-Cycloserine T0 0 cell MCF001089_TD19 +-4.205021 -0.692778 0.222305 1.352186 -0.581771 -0.490783 0.027384 0.0 L-Cyc_cell_T0-2 L-Cycloserine T0 0 cell MCF001089_TD20 +-5.80631 0.441183 0.660591 -0.656464 0.098959 0.278277 0.454242 0.0 L-Cyc_cell_T2h-1 L-Cycloserine T2h 2 cell MCF001089_TD25 +1.829954 1.903895 -0.556645 0.87951 1.16872 -0.001079 0.024794 0.0 L-Cyc_cell_T2h-2 L-Cycloserine T2h 2 cell MCF001089_TD26 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--cell_var.svg --- a/test-data/abundances--cell_var.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--cell_var.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.022373 + 2024-03-26T10:28:20.721169 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -43,7 +43,7 @@ L 97.776 54.144 L 62.064 54.144 z -" clip-path="url(#pc8c9f6ba16)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> +" clip-path="url(#p9ba8cd025a)" style="fill: #679698"/> - - + @@ -183,7 +183,7 @@ - + @@ -224,7 +224,7 @@ - + @@ -273,7 +273,7 @@ - + @@ -309,7 +309,7 @@ - + @@ -351,7 +351,7 @@ - + @@ -398,7 +398,7 @@ - + @@ -425,7 +425,7 @@ - + @@ -490,12 +490,12 @@ - - + @@ -531,7 +531,7 @@ - + @@ -545,7 +545,7 @@ - + @@ -559,7 +559,7 @@ - + @@ -573,7 +573,7 @@ - + @@ -587,7 +587,7 @@ - + @@ -601,7 +601,7 @@ - + @@ -615,7 +615,7 @@ - + @@ -990,28 +990,28 @@ - + - + - + - + - + - + - + - + + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--cell_var.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--cell_var.tsv Wed Mar 27 16:53:11 2024 +0000 @@ -0,0 +1,9 @@ +Explained Variance % PC +72.096685 PC1 +15.316109 PC2 +7.954519 PC3 +2.461762 PC4 +1.311833 PC5 +0.612223 PC6 +0.246869 PC7 +0.0 PC8 diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--med--label-n_pc.svg --- a/test-data/abundances--med--label-n_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--med--label-n_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.540670 + 2024-03-26T10:28:21.148615 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,30 +37,26 @@ z " style="fill: #ffffff"/> - - - - +" clip-path="url(#p3049e9e9ca)" style="fill: none; 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stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p3049e9e9ca)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p3049e9e9ca)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> +" clip-path="url(#p3049e9e9ca)" style="fill: #ff7f0e; stroke: #ffffff; stroke-width: 0.715542"/> + + + + + + + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -823,22 +826,22 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -950,9 +953,10 @@ + - + - + - +" style="stroke: #ffffff; stroke-width: 0.715542"/> - + @@ -1060,25 +1064,25 @@ - + - +" style="stroke: #ffffff; stroke-width: 0.715542; stroke-linejoin: miter"/> - + @@ -1114,7 +1118,7 @@ - + diff -r b6faa1142f83 -r 76c2567165fa test-data/abundances--med--label-y_pc.svg --- a/test-data/abundances--med--label-y_pc.svg Mon Mar 04 19:56:22 2024 +0000 +++ b/test-data/abundances--med--label-y_pc.svg Wed Mar 27 16:53:11 2024 +0000 @@ -6,11 +6,11 @@ - 2023-10-08T10:14:24.489990 + 2024-03-26T10:28:21.111584 image/svg+xml - Matplotlib v3.7.3, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -37,30 +37,26 @@ z " style="fill: #ffffff"/> - - - - +" clip-path="url(#pcf08ee3233)" style="fill: none; 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