Update the OPTIONS_TXT/output of make_tracks_file

docs/content/tracks/auto/bed_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # If the bed file contains the exon
@@ -15,7 +16,7 @@ height = 2
 # If the bed file contains a column for color (column 9), then this color can be used by
 # setting:
 # color = bed_rgb
-#if color is a valid colormap name (like RbBlGn), then the score is mapped
+#if color is a valid colormap name (like RbBlGn), then the score (column 5) is mapped
 # to the colormap.
 # In this case, the the min_value and max_value for the score can be provided, otherwise
 # the maximum score and minimum score found are used.
@@ -24,8 +25,6 @@ height = 2
 #max_value=100
 # If the color is simply a color name, then this color is used and the score is not considered.
 color = darkblue
-# height of track in cm
-height = 5
 # whether printing the labels
 labels = false
 # optional:
@@ -37,21 +36,24 @@ fontsize = 10
 # optional: line_width
 #line_width = 0.5
 # the display parameter defines how the bed file is plotted.
-# The options are ['collapsed', 'interleaved', 'triangles'] These options asume that the regions do not overlap.
+# Default is 'stacked' where regions are plotted on different lines so
+# we can see all regions and all labels.
+# The other options are ['collapsed', 'interleaved', 'triangles']
+# These options assume that the regions do not overlap.
 # `collapsed`: The bed regions are plotted one after the other in one line.
 # `interleaved`: The bed regions are plotted in two lines, first up, then down, then up etc.
-# if display is not given, then each region is plotted using the gene style
 # optional, default is black. To remove the border, simply set 'border_color' to none
 # Not used in tssarrow style
 #border_color = black
-# style to plot the genes when they have exon information
+# style to plot the genes when the display is not triangles
 #style = UCSC
 #style = flybase
 #style = tssarrow
 # maximum number of gene rows to be plotted. This
 # field is useful to limit large number of close genes
 # to be printed over many rows. When several images want
-# to be combined this must be set to get equal size, otherwise, on each image the height of each gene changes
+# to be combined this must be set to get equal size
+# otherwise, on each image the height of each gene changes
 #gene_rows = 10
 # by default the ymax is the number of
 # rows occupied by the genes in the region plotted. However,
@@ -81,9 +83,6 @@ fontsize = 10
 # If you want that the tip of the arrow correspond to
 # the extremity of the interval use:
 # arrowhead_included = true
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
-#overlay_previous = yes
 # optional. If not given is guessed from the file ending.
 file_type = bed
 

docs/content/tracks/auto/bedgraph_matrix_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # a bedgraph matrix file is like a bedgraph, except that per bin there
@@ -23,7 +24,8 @@ type = lines
 # If the type is not lines, you can choose to keep the matrix as not rasterized
 # (only used if you use pdf or svg output format) by using:
 # rasterize = false
-# The different options for color maps can be found here: https://matplotlib.org/users/colormaps.html
+# The different options for color maps can be found here:
+# https://matplotlib.org/users/colormaps.html
 # the default color map is viridis
 # If you want your own colormap you can put the values of the color you want
 # For example, colormap = ['blue', 'yellow', 'red']

docs/content/tracks/auto/bedgraph_options_text.txt

@@ -5,16 +5,19 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 color = green
+# To use a different color for negative values
+#negative_color = red
 # To use transparency, you can use alpha
 # default is 1
 # alpha = 0.5
 # the default for min_value and max_value is 'auto' which means that the scale will go
-# from the minimum value found in the region plotted to the maximum value found.
+# roughly from the minimum value found in the region plotted to the maximum value found.
 min_value = 0
 #max_value = auto
 # to convert missing data (NaNs) into zeros. Otherwise, missing data is not plotted.

docs/content/tracks/auto/bigwig_options_text.txt

@@ -5,19 +5,23 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 color = #666666
+# To use a different color for negative values
+#negative_color = red
 # To use transparency, you can use alpha
 # default is 1
 # alpha = 0.5
 # the default for min_value and max_value is 'auto' which means that the scale will go
-# from the minimum value found in the region plotted to the maximum value found.
+# roughly from the minimum value found in the region plotted to the maximum value found.
 min_value = 0
 #max_value = auto
-# The number of bins takes the region to be plotted and divides it into the number of bins specified
+# The number of bins takes the region to be plotted and divides it
+# into the number of bins specified
 # Then, at each bin the bigwig mean value is computed and plotted.
 # A lower number of bins produces a coarser tracks
 number_of_bins = 700

docs/content/tracks/auto/domains_options_text.txt

@@ -5,17 +5,15 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
-# If the bed file contains the exon
-# structure (bed 12) then this is plotted. Otherwise
-# a region **with direction** is plotted.
 # If the bed file contains a column for color (column 9), then this color can be used by
 # setting:
 # color = bed_rgb
-#if color is a valid colormap name (like RbBlGn), then the score is mapped
+#if color is a valid colormap name (like RbBlGn), then the score (column 5) is mapped
 # to the colormap.
 # In this case, the the min_value and max_value for the score can be provided, otherwise
 # the maximum score and minimum score found are used.
@@ -24,66 +22,10 @@ height = 2
 #max_value=100
 # If the color is simply a color name, then this color is used and the score is not considered.
 color = darkblue
-# height of track in cm
-height = 5
-# whether printing the labels
-labels = false
-# optional:
-# by default the labels are not printed if you have more than 60 features.
-# to change it, just increase the value:
-#max_labels = 60
-# optional: font size can be given to override the default size
-fontsize = 10
 # optional: line_width
 #line_width = 0.5
-# the display parameter defines how the bed file is plotted.
-# The options are ['collapsed', 'interleaved', 'triangles'] These options asume that the regions do not overlap.
-# `collapsed`: The bed regions are plotted one after the other in one line.
-# `interleaved`: The bed regions are plotted in two lines, first up, then down, then up etc.
-# if display is not given, then each region is plotted using the gene style
 # optional, default is black. To remove the border, simply set 'border_color' to none
-# Not used in tssarrow style
 #border_color = black
-# style to plot the genes when they have exon information
-#style = UCSC
-#style = flybase
-#style = tssarrow
-# maximum number of gene rows to be plotted. This
-# field is useful to limit large number of close genes
-# to be printed over many rows. When several images want
-# to be combined this must be set to get equal size, otherwise, on each image the height of each gene changes
-#gene_rows = 10
-# by default the ymax is the number of
-# rows occupied by the genes in the region plotted. However,
-# by setting this option, the global maximum is used instead.
-# This is useful to combine images that are all consistent and
-# have the same number of rows.
-#global_max_row = true
-# If you want to plot all labels inside the plotting region:
-#all_labels_inside = true
-# If you want to display the name of the gene which goes over the plotted
-# region in the right margin put:
-#labels_in_margin = true
-# if you use UCSC style, you can set the relative distance between 2 arrows on introns
-# default is 2
-#arrow_interval = 2
-# if you use tssarrow style, you can choose the length of the arrow in bp
-# (default is 4% of the plotted region)
-#arrow_length = 5000
-# if you use flybase or tssarrow style, you can choose the color of non-coding intervals:
-#color_utr = grey
-# as well as the proportion between their height and the one of coding
-# (by default they are the same height):
-#height_utr = 1
-# By default, for oriented intervals in flybase style,
-# or bed files with less than 12 columns, the arrowhead is added
-# outside of the interval.
-# If you want that the tip of the arrow correspond to
-# the extremity of the interval use:
-# arrowhead_included = true
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
-#overlay_previous = yes
 # optional. If not given is guessed from the file ending.
-file_type = bed
+file_type = domains
 

docs/content/tracks/auto/epilogos_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # The categories file should contain the color information for each category id

docs/content/tracks/auto/gtf_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # By default the transcript_name is used.
@@ -30,21 +31,24 @@ fontsize = 10
 # optional: line_width
 #line_width = 0.5
 # the display parameter defines how the gtf file is plotted.
-# The options are ['collapsed', 'interleaved', 'triangles'] These options asume that the regions do not overlap.
+# Default is 'stacked' where regions are plotted on different lines so
+# we can see all regions and all labels.
+# The other options are ['collapsed', 'interleaved', 'triangles']
+# These options assume that the regions do not overlap.
 # `collapsed`: The gtf regions are plotted one after the other in one line.
 # `interleaved`: The gtf regions are plotted in two lines, first up, then down, then up etc.
-# if display is not given, then each region is plotted using the gene style
 # optional, default is black. To remove the border, simply set 'border_color' to none
 # Not used in tssarrow style
 #border_color = black
-# style to plot the genes when they have exon information
+# style to plot the genes when the display is not triangles
 #style = UCSC
 #style = flybase
 #style = tssarrow
 # maximum number of gene rows to be plotted. This
 # field is useful to limit large number of close genes
 # to be printed over many rows. When several images want
-# to be combined this must be set to get equal size, otherwise, on each image the height of each gene changes
+# to be combined this must be set to get equal size
+# otherwise, on each image the height of each gene changes
 #gene_rows = 10
 # by default the ymax is the number of
 # rows occupied by the genes in the region plotted. However,
@@ -74,9 +78,6 @@ fontsize = 10
 # If you want that the tip of the arrow correspond to
 # the extremity of the interval use:
 # arrowhead_included = true
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
-#overlay_previous = yes
 # optional. If not given is guessed from the file ending.
 file_type = gtf
 

docs/content/tracks/auto/hic_matrix_options_text.txt

@@ -1,6 +1,6 @@
 
-title =
-# The different options for color maps can be found here: https://matplotlib.org/users/colormaps.html
+# The different options for color maps can be found here:
+# https://matplotlib.org/users/colormaps.html
 # the default color map is RdYlBu_r (_r) stands for reverse
 # If you want your own colormap you can put the values of the color you want
 # For example, colormap = ['blue', 'yellow', 'red']
@@ -10,7 +10,8 @@ title =
 # If it is more than 125% of the plotted region, it will
 # be adjsted to this maximum value.
 depth = 100000
-# height of track (in cm) can be given. Otherwise, the height is computed such that the proportions of the
+# height of track (in cm) can be given.
+# Otherwise, the height is computed such that the proportions of the
 # hic matrix are kept (e.g. the image does not appear shrink or extended)
 # height = 10
 # min_value and max_value refer to the contacts in the matrix.
@@ -23,8 +24,6 @@ transform = log1p
 # the default is to extend neighboring bins to
 # obtain an aesthetically pleasant output
 show_masked_bins = false
-# if you want to plot the track upside-down:
-# orientation = inverted
 # optional if the values in the matrix need to be scaled the
 # following parameter can be used. This is useful to plot multiple hic-matrices on the same scale
 # scale_factor = 1

docs/content/tracks/auto/hlines_options_text.txt

@@ -5,15 +5,20 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # color of the lines
 color = black
 # To use transparency, you can use alpha
 # default is 1
 # alpha = 0.5
+# the default for min_value and max_value is 'auto' which means that the scale will go
+# roughly from the minimum value found in the region plotted to the maximum value found.
+min_value = 0
+#max_value = auto
 # line width:
 # line_width = 0.5
 # options for line_style are 'solid', 'dashed', 'dotted', and 'dashdot'

docs/content/tracks/auto/links_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # the file format for links is (tab separated)
@@ -18,8 +19,8 @@ height = 2
 # depending on the value of links_type either 'arcs' or 'triangles' or 'loops' can be plotted.
 # If arcs, a line will be drawn from the center of the first region (chr1: 150),
 # to the center of the other region (chr1: 275).
-# if triangles, the vertix of the triangle will be drawn at the center between the two points (also the center of
-# each position is used)
+# if triangles, the vertix of the triangle will be drawn at the center between the two points
+# (also the extremity of each position is used)
 # if loops, a rectangle highlighting the intersection between the 2 regions will be shown
 # the triangles, and loops options are convenient to overlay over a
 # Hi-C matrix to highlight the matrix pixel of the highlighted link

docs/content/tracks/auto/narrow_peak_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 color = #FF000080

docs/content/tracks/auto/scalebar_options_text.txt

@@ -5,8 +5,9 @@ title =
 height = 2
 # if you want to plot the track upside-down:
 # orientation = inverted
-# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'. For the 'share-y'
-# option the y axis values is shared between this plot and the overlay plot. Otherwise, each plot use its own scale
+# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
+# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
+# Otherwise, each plot use its own scale
 #overlay_previous = yes
 
 # color of the scalebar