ibowankenobi-i-pv

show_links = yes show_highlights = yes show_text = yes show_heatmaps = yes show_scatter = yes show_histogram = yes <<include karyotype.and.layout.conf>> ### links <links> show = conf(show_links) ribbon = yes flat = yes radius = 0.45r-55p bezier_radius = 0r color = black_a5 <link> file = data/rn.bundle.txt <<include link.rules.conf>> </link> <link> file = data/mm.bundle.txt <<include link.rules.conf>> </link> </links> ### plots <plots> <<include highlights.conf>> # some large human genes (list contains genes > 250kb in size) <plot> show = conf(show_text) type = text file = data/genes.txt color = black r1 = 0.73r r0 = 0.415r label_size = 9p label_font = condensed rpadding = 0r padding = 0r label_snuggle = yes max_snuggle_distance = 1r snuggle_sampling = 1 snuggle_tolerance = 0.25r show_links = yes link_dims = 4p,2p,5p,2p,2p link_thickness = 2p link_color = grey <rules> <rule> condition = var(value) =~ /omim/ color = blue flow = continue </rule> <rule> condition = var(value) =~ /cancer/ color = red label_font = bold flow = continue </rule> <rule> # remove trailing _.* from label condition = 1 value = eval(replace(var(value),qr/_.*/,"")) </rule> </rules> </plot> # human->mouse and human->rat chain heatmaps <plot> show = conf(show_heatmaps) type = heatmap file = data/heatmap.hs.mm.20e6.txt # this is a 9-color Brewer blues sequential palette # see etc/colors.brewer.lists.conf for color list definitions and # etc/colors.brewer.conf for Brewer color RGB definitions color = blues-9-seq min = 0 max = .20e6 r0 = 0.765r r1 = 0.785r stroke_color = white stroke_thickness = 1p </plot> <plot> show = conf(show_heatmaps) type = heatmap file = data/heatmap.hs.rn.20e6.txt # this is a 9-color Brewer reds sequential palette color = reds-9-seq min = 0 max = .20e6 r0 = 0.79r r1 = 0.81r stroke_color = white stroke_thickness = 1p </plot> <plot> show = conf(show_heatmaps) type = heatmap file = data/heatmap.hs.mm.10e6.txt color = blues-9-seq min = 0 max = .10e6 r0 = 0.895r r1 = 0.915r stroke_color = white stroke_thickness = 1p </plot> <plot> show = conf(show_heatmaps) type = heatmap file = data/heatmap.hs.rn.10e6.txt color = reds-9-seq min = 0 max = .10e6 r0 = 0.92r r1 = 0.94r stroke_color = white stroke_thickness = 1p </plot> <<include mmchain.heatmap.allchrs.conf>> <<include rnchain.heatmap.allchrs.conf>> <<include rnchain.scatter.allchrs.conf>> <<include mmchain.scatter.allchrs.conf>> ################################################################ # histograms on human chromosomes # total mouse chain, with scatter plot # oriented outward <plot> show = conf(show_histogram) type = histogram file = data/heatmap.hs.mm.20e6.txt min = 0 max = .5e6 fill_under = yes # 4th color in 5-color blues sequential palette with # transparency (_aN means N/6% transparency (5/6 = 83%). fill_color = blues-5-seq-4_a5 r0 = 1r r1 = 1r+180p orientation = out <backgrounds> show = data <background> color = vvlgrey y0 = 0.4r y1 = 0.6r </background> </backgrounds> <axes> show = data thickness = 1 <axis> spacing = 0.05r color = vlgrey position_skip = 0.25r,0.35r </axis> <axis> spacing = 0.1r y0 = 0.3r y1 = 0.7r color = grey </axis> <axis> position = .3e6,0.55r color = red thickness = 2 </axis> </axes> </plot> <plot> show = conf(show_scatter) type = scatter file = data/heatmap.hs.mm.5e6.txt r1 = 1r+180p r0 = 1r max = .5e6 min = 0 glyph = square glyph_size = 6 color = undef stroke_color = blues-5-seq-5 stroke_thickness = 1 </plot> # total rat chain, with scatter plot # oriented inward <plot> show = conf(show_histogram) type = histogram file = data/heatmap.hs.rn.20e6.txt r1 = 1r+180p r0 = 1r max = .5e6 min = 0 fill_under = yes fill_color = reds-5-seq-4_a5 orientation = in </plot> <plot> show = conf(show_scatter) type = scatter file = data/heatmap.hs.rn.5e6.txt r1 = 1r+180p r0 = 1r max = .5e6 min = 0 glyph = triangle glyph_size = 8 color = reds-5-seq-5 orientation = in </plot> </plots> <<include ideogram.conf>> <<include ticks.conf>> <image> <<include etc/image.conf>> </image> # includes etc/colors.conf # etc/fonts.conf # etc/patterns.conf <<include etc/colors_fonts_patterns.conf>> # system and debug settings <<include etc/housekeeping.conf>> data_out_of_range* = trim # If you experience strange artefacts in the image (spurious squares), # turn anti aliasing off. This behaviour is due to a bug in some # versions of libgd. #anti_aliasing* = no