update

README.md

@@ -13,6 +13,8 @@
 - you can draw crosslink or sysnteny among features of different tracks<br><br>
 
 ### update feture:<br>
+#### 2018-12-10:<br>
+- add  plot depth and pabio read mapping of bam file, as example/out11.svg or out10.svg <br>
 #### 2018-11-12:<br>
 - rewrite feature.crossing.link.conf so that defined color and opactity or order or anchor position of every pair of links.<br>
 - add tracks_reorder to plot tracks by new order, otherwise you must adjust --list file <br>
@@ -35,15 +37,12 @@
 &nbsp;&nbsp;&nbsp;&nbsp;5. embed svg in svg to make heatmap or scatter or line or histogram more easy to product, like example/out.svg*svg or \<foreignObject\> <br> <br>
 
 
-#### denpence <br>
-```
-perl
-Bio::DB::Sam ( install with cpan)
-```
-<br>
-
 
 
+![gene cluster image](example/out11.svg)
+<br><br><br>
+![gene cluster image](example/out10.svg)
+<br><br><br>
 ![gene cluster image](example/out.svg)
 <br><br><br>
 ![gene cluster image](example/out2.svg)
@@ -52,8 +51,6 @@ Bio::DB::Sam ( install with cpan)
 <br><br>
 ![gene cluster image](example/out3.2.svg)
 <br><br>
-![gene cluster image](example/out10.svg)
-<br><br><br>
 ![gene cluster image](example/out6.svg)
 <br><br><br>
 ![gene cluster image](example/out8.svg)

example/feature.color.label.conf11

@@ -0,0 +1 @@
+

example/list6

@@ -1,6 +1,2 @@
-s1.s1000	s1.gff	s1.seq	s1000	1	2000
-s1.s10000.0-2k	s1.gff	s1.seq	s10000	1	2000
-s1	s1.gff	s1.seq	s1	1+1	3000+50	s1	3000	6000+10	s1	6000-20	10000	s1000	2000	6000	s10000	2000	6000	s10000	6000	10000
-s2	s2.gff	s2.seq	s2	1	9000	s2000	2000	6000	s20000	2000	6000	s20000	6000	10000
-s3	s3.gff	s3.seq	s3	1+10	5000+100	s3	3000	6000	s3	6000	10000	s3000	2000	6000	s30000	2000	6000
-s4	s4.gff	s4.seq	s4000	2000	6000	s40000	1000	8000	s40000	8000	10000
+# download chr14.fa from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr14.fa.gz
+chr14	chr14.gff	../../genomeview/chr14.fa	14	66901400	66901400+1000

example/list6.new

@@ -0,0 +1 @@
+chr14	chr14.gff,chr14.read_mapping.gff	../../genomeview/chr14.fa	14	66901400	66901400+1000

example/main.10.conf

@@ -1,5 +1,5 @@
 # output figure size
-svg_width_height = 1500,1200 # *
+svg_width_height = 1500,500 # *
 pdf_dpi = 100
 svg_background_color = white #background color of whole figure
 
@@ -21,13 +21,13 @@ feature_label_color=black
 feature_shift_y=0 # unit is feature_shift_y_unit 
 feature_shift_y_unit=backbone # backbone or radius or percent, backbone is genome_height_ratio
 feature_shift_x=0 # unit is bp
-feature_height_ratio= 1 # defined feature height
+feature_height_ratio=3 # defined feature height
 track_style= fill:blue;opacity:0.2 # fill:blue;stroke:pink;stroke-width:5;fill-opacity:0.1;stroke-opacity:0.9
 feature_color=rgb(50,205,50)
 feature_border_size=0
 feature_border_color=black 
-genome_height_ratio=0.2 # mean genome height extend ratio
-feature_arrow_sharp_extent=0 # bigger mean sharper arrow
+genome_height_ratio=1 # mean genome height extend ratio
+feature_arrow_sharp_extent=1 # bigger mean sharper arrow
 # order for display
 track_order=1
 feature_order=2
@@ -80,7 +80,7 @@ legend_stroke_color=black
 legend_stroke_width=0.5
 
 # crossling among features
-crossing_link = feature.crossing.link.conf9.new
+crossing_link = feature.crossing.link.conf10
 cross_link_color = #FF8C00
 cross_link_opacity = 1
 cross_link_anchor_pos = low_up # up,medium,low
@@ -118,21 +118,21 @@ scale_tick_fontsize=13
 #$sample,$scf,$block_flag,$window_size,$depth_file,$yaxis,$ytick_flag,$yaxis_show,$ytick_label,$hgrid_flag,$tick_color,$tick_opacity,$tick_border,$label_size
 
 
-plot_depth = hist,1,s3,s3,1,100,s3.s3.depth.txt,5->55,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	highlight_hgrid->26:2:green,28:2:black    highlight_columns->0:20:green:0.7,20:100:black:0.5 start_end_xaxis->111:511,711:1111,1211:1911
-plot_depth = hist,1,s3,s3,1,100,s3.s3.depth.txt,65->95,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,2:2
-plot_depth = hist,1,s3,s3,2,100,s3.s3.depth.txt,15->70,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:green,0.6:0.3,0.3:0.3,3:3
+plot_depth = hist,1,s3,s3,1,100,s3.s3.depth.txt,5->55,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,5:5:2:0.2,3:3	highlight_hgrid->26:2:green,28:2:black    highlight_columns->0:20:green:0.7,20:100:black:0.5 start_end_xaxis->111:511,711:1111,1211:1911
+plot_depth = hist,1,s3,s3,1,100,s3.s3.depth.txt,65->95,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,5:5:2:0.2,2:2
+plot_depth = hist,1,s3,s3,2,100,s3.s3.depth.txt,15->70,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:green,0.6:0.3,5:5:2:0.2,3:3
 
-plot_depth = scatter,1,s3,s3,3,50,s3.s3.depth.txt,5->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
-plot_depth = scatter_line,1,s3,s3,3,50,s3.s3.depth.txt,5->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
-plot_depth = hist,1,s3,s3,3,50,s3.s3.depth.txt,55->90,ytick_flag,10->30->4,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+plot_depth = scatter,1,s3,s3,3,50,s3.s3.depth.txt,5->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,black:green,1:0.3,5:5:2:0.2,3:3
+plot_depth = scatter_line,1,s3,s3,3,50,s3.s3.depth.txt,5->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,black:green,1:0.3,5:5:2:0.2,3:3
+plot_depth = hist,1,s3,s3,3,50,s3.s3.depth.txt,55->90,ytick_flag,10->30->4,ytick_label_text,hgrid_flag,black:green,1:0.3,5:5:2:0.2,3:3
 
 #plot_depth = hist,1,s3,s3,3,50,s3.s3.depth.txt,-55->-90,ytick_flag,10->30->4,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
 
-plot_depth = hist,1,s2,s2,1,50,../data/s2.seq.sam.sorted.bam,15->80,ytick_flag,10->120->10,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+plot_depth = hist,1,s2,s2,1,50,../data/s2.seq.sam.sorted.bam,15->80,ytick_flag,10->120->10,ytick_label_text,hgrid_flag,black:green,1:0.3,5:5:2:0.2,3:3
 
-reads_mapping=long_reads,1,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,55->85,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	 start_end_xaxis->3000:4000,4500:5500
-reads_mapping=long_reads,1,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,20->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	 start_end_xaxis->2000:6000
-reads_mapping=long_reads,1,s2,s20000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,23->80,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	 start_end_xaxis->2000:6000
+reads_mapping=long_reads,1,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,55->85,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,5:5:2:0.2,3:3	 start_end_xaxis->3000:4000,4500:5500
+reads_mapping=long_reads,1,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,20->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,5:5:2:0.2,3:3	 start_end_xaxis->2000:6000
+reads_mapping=long_reads,1,s2,s20000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,23->80,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,5:5:2:0.2,3:3	 start_end_xaxis->2000:6000
 
 
 

example/main.11.conf

@@ -0,0 +1,140 @@
+# output figure size
+svg_width_height = 1000,800 # *
+pdf_dpi = 100
+svg_background_color = white #background color of whole figure
+
+# plot feature type
+feature_keywords = gene,circle,ytick,plot_depth,long_read,xxxxx # *, gene,point,hist,heatmap
+feature_setting = feature.color.label.conf11.new # *
+
+# figure width layout
+width_ratio_ref_cluster_legend = 0.1-0.75-0.15 # 0.1+0.75+0.15=1
+
+
+
+
+## global setting start, specific setting in feature_setting
+feature_shape=arrow  # only arrow, rect for figure shape, not support round_rect and circle_point yet
+feature_arrow_width_extent=0.3
+feature_label_size=10
+feature_label_color=black
+feature_shift_y=0 # unit is feature_shift_y_unit 
+feature_shift_y_unit=backbone # backbone or radius or percent, backbone is genome_height_ratio
+feature_shift_x=0 # unit is bp
+feature_height_ratio=5 # defined feature height
+feature_height_unit=percent
+track_style= fill:blue;opacity:0.2 # fill:blue;stroke:pink;stroke-width:5;fill-opacity:0.1;stroke-opacity:0.9
+feature_color=rgb(50,205,50)
+feature_border_size=0
+feature_border_color=black 
+genome_height_ratio=5 # mean genome height extend ratio
+feature_arrow_sharp_extent=0 # bigger mean sharper arrow
+# order for display
+track_order=1
+feature_order=2
+feature_label_order=4
+cross_link_order=0 # bigger mean upper 
+display_feature=yes # no or yes
+# whether dispaly feature label
+display_feature_label=no # yes or no or yes,no or no,yes
+# feature_label 9 kinds of positon
+pos_feature_label=right_low # or medium_low or left_low or right_low or medium_medium or left_medium
+# padding between feature and label
+# padding between feature and label
+padding_feature_label = 0.01 # space between feature and label
+# freature label rotate angle
+label_rotate_angle=0
+feature_label_auto_angle_flag=1 # if auto shift angle
+# display or conceal the connect line between same scaffold
+connect_with_same_scaffold=no
+connect_stroke_dasharray=2,5
+connect_stroke_width=2
+connect_stroke_color=black
+absolute_postion_in_title=yes
+## global setting end, specific setting in feature_setting
+
+
+
+# if less this, will trigger auto shift feature label
+distance_closed_feature=200 # xxbp, if the distancetwo feature is too close, so sparate with shift_angle_closed_feature
+shift_angle_closed_feature = 10
+
+# layout
+top_bottom_margin = 0.2 # 高度上 top和bottom占的比例,top和bottom可能有scale
+space_between_blocks = 500 # bp, mean space of every block in one track
+default_legend = other
+
+# new sample name
+#sample_name_old2new = sample.name.new.conf
+sample_name_color_default = black
+sample_name_font_size_default = 15 
+
+
+# legend
+display_legend=yes # yes or other
+legend_font_size = 20 #legend中文字字体大小
+legend_height_ratio = 0.7 # compare with feature height
+legend_width_margin = 0.15 # legends左右两侧的margin
+legend_height_space = 0.1
+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
+legend_stroke_color=black
+legend_stroke_width=0.5
+
+# crossling among features
+#crossing_link = feature.crossing.link.conf9.new
+cross_link_color = #FF8C00
+cross_link_opacity = 1
+cross_link_anchor_pos = low_up # up,medium,low
+ignore_sharp_arrow=no # yes or no
+cross_link_orientation_ellipse=up
+cross_link_shape=quadrilateral # ellipse or w or quadrilateral or line
+cross_link_height_ellipse=10,8 # 10 and 8 is the radius of outter ellipse and inner ellipse
+
+
+
+#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 )
+#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
+
+# scale
+scale_display=yes # yes or no
+scale_position=low # up or low or up_low
+scale_color=green
+scale_width=0.5
+scale_ratio=100 # bp
+scale_padding_y=0.6
+scale_tick_opacity=1
+scale_tick_height=0.01
+scale_order=-1
+scale_tick_padding_y=10
+scale_tick_fontsize=13
+
+
+# 3rd column: 0 mean all fragment, otherwise 1 mean 1st fragment in the track
+# forth column mean depth window size bp
+# bam or dep.txt
+# 10 -> 50 or -10 -> -50
+# 20->30 is for show
+#depth_hist = s2,s2000,0,100,path_map.sort.bam,0->50,ytick_flag,20->30,ytick_label_text,hgrid_flag,black:black,1:0.3,1:0.5
+#depth_hist = s2,s2000,0,100,path_map.sort.bam,60->90,ytick_flag,20->30,ytick_label_text,hgrid_flag,green:green,1:0.3,1:0.5
+#$sample,$scf,$block_flag,$window_size,$depth_file,$yaxis,$ytick_flag,$yaxis_show,$ytick_label,$hgrid_flag,$tick_color,$tick_opacity,$tick_border,$label_size
+
+
+#plot_depth = hist,1,s3,s3,1,100,s3.s3.depth.txt,5->55,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	highlight_hgrid->26:2:green,28:2:black    highlight_columns->0:20:green:0.7,20:100:black:0.5 start_end_xaxis->111:511,711:1111,1211:1911
+#plot_depth = hist,1,s3,s3,1,100,s3.s3.depth.txt,65->95,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,2:2
+#plot_depth = hist,1,s3,s3,2,100,s3.s3.depth.txt,15->70,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:green,0.6:0.3,0.3:0.3,3:3
+
+#plot_depth = scatter,1,s3,s3,3,50,s3.s3.depth.txt,5->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+#plot_depth = scatter_line,1,s3,s3,3,50,s3.s3.depth.txt,5->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+#plot_depth = hist,1,s3,s3,3,50,s3.s3.depth.txt,55->90,ytick_flag,10->30->4,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+
+#plot_depth = hist,1,s3,s3,3,50,s3.s3.depth.txt,-55->-90,ytick_flag,10->30->4,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+
+#plot_depth = hist,1,s2,s2,1,50,../data/s2.seq.sam.sorted.bam,15->80,ytick_flag,10->120->10,ytick_label_text,hgrid_flag,black:green,1:0.3,0.3:0.3,3:3
+
+#reads_mapping=long_reads,1,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,55->85,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	 start_end_xaxis->3000:4000,4500:5500
+#reads_mapping=long_reads,1,s2,s2000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,20->50,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	 start_end_xaxis->2000:6000
+#reads_mapping=long_reads,1,s2,s20000,0,../data/s2.seq.longreads.map2ref.sort.bam,rainbow_or_hline,23->80,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:0.5,0.3:0.3,3:3	 start_end_xaxis->2000:6000
+reads_mapping=long_reads,1,chr14,14,0,../../genomeview/genomeview/examples/data/pacbio.chr14.sort.bam,rainbow_or_hline,15->1250,ytick_flag,20->30->2,ytick_label_text,hgrid_flag,green:black,1:1,3:10:2:0,15:15 # $tick_color, $tick_opacity, $tick_border, tick_label_size
+tracks_shift_y=chr14,0,+12 #sample2,block_index2,+0.3;sample2,block_index2,-0.1
+
+

example/main.conf

@@ -20,8 +20,8 @@ feature_height_ratio=4
 feature_opacity=0.8
 track_style=fill:blue # green or #02030
 feature_color = rgb(50,205,50)
-genome_height_ratio=0.5 # mean genome height extend ratio
-feature_arrow_sharp_extent=0 # bigger mean sharper arrow
+genome_height_ratio=1 # mean genome height extend ratio
+feature_arrow_sharp_extent=1 # bigger mean sharper arrow
 # order for display
 track_order=1
 feature_order=2