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| 1 | + |
| 2 | +###############################----This Is wanted, 如果要画read mapping下面参数是必须的----############################## |
| 3 | + |
| 4 | +synteny = order->0->1,query->pO83_CORR.indel.blast:target->pO83_CORR,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6,blast_m8,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1 |
| 5 | +synteny = order->0->1,query->pO83_CORR.indel.blast:target->pO83_CORR.twin.minimap,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.paf.gz,paf,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1 |
| 6 | + |
| 7 | + |
| 8 | +feature_id_is_unique = no |
| 9 | +display_segment_name=yes,center,shift_y:+2,fontsize:6,color:black,order:5,rotate:0 |
| 10 | +display_segment_strand=5:5",3:3",color:black,fontsize:10 |
| 11 | + |
| 12 | + |
| 13 | + |
| 14 | + |
| 15 | + |
| 16 | + |
| 17 | + |
| 18 | + |
| 19 | + |
| 20 | + |
| 21 | + |
| 22 | + |
| 23 | + |
| 24 | + |
| 25 | +##############################----This Is Optional,下面是可选的，可以用默认值----############################## |
| 26 | + |
| 27 | +# output figure size |
| 28 | +svg_width_height = 1300,500 # * |
| 29 | +pdf_dpi = 100 |
| 30 | +svg_background_color = white #background color of whole figure |
| 31 | + |
| 32 | +# plot feature type |
| 33 | +feature_keywords = xx # *, gene,point,hist,heatmap |
| 34 | +feature_setting = feature.color.label.6.conf # * |
| 35 | + |
| 36 | +# figure width layout |
| 37 | +width_ratio_ref_cluster_legend = 0.1-0.75-0.15 # 0.1+0.75+0.15=1 |
| 38 | + |
| 39 | + |
| 40 | + |
| 41 | + |
| 42 | +## global setting start, specific setting in feature_setting |
| 43 | +feature_shape=arrow # only arrow, rect for figure shape, not support round_rect and circle_point yet |
| 44 | +feature_arrow_width_extent=30bp |
| 45 | +feature_label_size=10 |
| 46 | +feature_label_color=black |
| 47 | +feature_shift_y=0 # unit is feature_shift_y_unit |
| 48 | +feature_shift_y_unit=backbone # backbone or radius or percent, backbone is genome_height_ratio |
| 49 | +feature_shift_x=0 # unit is bp |
| 50 | +feature_height_ratio=3 # defined feature height |
| 51 | +feature_height_unit=backbone |
| 52 | +track_style= fill:blue;opacity:0.2 # fill:blue;stroke:pink;stroke-width:5;fill-opacity:0.1;stroke-opacity:0.9 |
| 53 | +feature_color=rgb(50,205,50) |
| 54 | +feature_border_size=0 |
| 55 | +feature_border_color=black |
| 56 | +genome_height_ratio=1 # mean genome height extend ratio |
| 57 | +feature_arrow_sharp_extent=0 # bigger mean sharper arrow |
| 58 | +# order for display |
| 59 | +track_order=1 |
| 60 | +feature_order=2 |
| 61 | +feature_label_order=4 |
| 62 | +cross_link_order=0 # bigger mean upper |
| 63 | +display_feature=yes # no or yes |
| 64 | +# whether dispaly feature label |
| 65 | +display_feature_label=no # yes or no or yes,no or no,yes |
| 66 | +# feature_label 9 kinds of positon |
| 67 | +pos_feature_label=right_low # or medium_low or left_low or right_low or medium_medium or left_medium |
| 68 | +# padding between feature and label |
| 69 | +# padding between feature and label |
| 70 | +y_margin_feature_label = 0.01 # space between feature and label |
| 71 | +# freature label rotate angle |
| 72 | +label_rotate_angle=0 |
| 73 | +feature_label_auto_angle_flag=1 # if auto shift angle |
| 74 | +# display or conceal the connect line between same scaffold |
| 75 | +connect_with_same_scaffold=no |
| 76 | +connect_stroke_dasharray=2,5 |
| 77 | +connect_stroke_width=2 |
| 78 | +connect_stroke_color=black |
| 79 | +absolute_postion_in_title=yes |
| 80 | +## global setting end, specific setting in feature_setting |
| 81 | + |
| 82 | + |
| 83 | + |
| 84 | +# if less this, will trigger auto shift feature label |
| 85 | +distance_closed_feature=1 # xxbp, if the distancetwo feature is too close, so sparate with shift_angle_closed_feature |
| 86 | +shift_angle_closed_feature = 10 |
| 87 | + |
| 88 | +# layout |
| 89 | +top_bottom_margin = 0.2 # 高度上 top和bottom占的比例,top和bottom可能有scale |
| 90 | +space_between_blocks = 500 # bp, mean space of every block in one track |
| 91 | +default_legend = other |
| 92 | + |
| 93 | +# new sample name |
| 94 | +#sample_name_old2new = sample.name.new.conf |
| 95 | +sample_name_color_default = black |
| 96 | +sample_name_font_size_default = 15 |
| 97 | + |
| 98 | + |
| 99 | +# legend |
| 100 | +display_legend=yes # yes or other |
| 101 | +legend_font_size = 20 #legend中文字字体大小 |
| 102 | +legend_height_ratio = 0.7 # compare with feature height |
| 103 | +legend_width_margin = 0.15 # legends左右两侧的margin |
| 104 | +legend_height_space = 0.1 |
| 105 | +legend_width_textpercent = 0.7 # legend内部的文字和arrow的比例，text是0.6则arrow是0.4 |
| 106 | +legend_stroke_color=black |
| 107 | +legend_stroke_width=0.5 |
| 108 | + |
| 109 | +# crossling among features |
| 110 | +#crossing_link = feature.crossing.link |
| 111 | +cross_link_color = #FF8C00 |
| 112 | +cross_link_opacity = 1 |
| 113 | +cross_link_anchor_pos = low_up # up,medium,low |
| 114 | +ignore_sharp_arrow=no # yes or no |
| 115 | +cross_link_orientation_ellipse=up |
| 116 | +cross_link_shape=quadrilateral # ellipse or w or quadrilateral or line |
| 117 | +cross_link_height_ellipse=10,8 # 10 and 8 is the radius of outter ellipse and inner ellipse |
| 118 | + |
| 119 | + |
| 120 | + |
| 121 | +#sort_by_one_feature = sort.feature # every track sort block's position by this feaure list(just only one feature for one track, if one traack not has one feature in this list , mean don't sort block's pos of this track ) |
| 122 | +#scaffold_order = order.list # if set this, will draw full-length of scaffold in gff, will ignore 4th col to last col of the --list |
| 123 | + |
| 124 | +# scale |
| 125 | +scale_display=yes # yes or no |
| 126 | +scale_position=low # up or low or up_low |
| 127 | +scale_color=green |
| 128 | +scale_width=0.5 |
| 129 | +scale_ratio=1700 # bp |
| 130 | +scale_padding_y=0.6 |
| 131 | +scale_tick_opacity=1 |
| 132 | +scale_tick_height=0.01 |
| 133 | +scale_order=-1 |
| 134 | +scale_tick_padding_y=10 |
| 135 | +scale_tick_fontsize=6 |
| 136 | + |
| 137 | + |
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