Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/circos/parse-table.conf @ 52:124b7fd92a3e draft
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author | davidvanzessen |
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date | Thu, 25 Feb 2021 13:36:15 +0000 |
parents | afe85eb6572e |
children | 81b3eb11ed2c |
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--- a/report_clonality/circos/parse-table.conf Thu Aug 08 07:40:36 2019 -0400 +++ b/report_clonality/circos/parse-table.conf Thu Feb 25 13:36:15 2021 +0000 @@ -1,391 +1,391 @@ - -################################################################ -# -# This is a fairly complicated configuration file. Take your time in -# experimenting and adjust one thing at a time :) -# -################################################################ - -max_col_num = 200 -max_row_num = 200 - -# skip this many rows before reading in header and data -skip_rows = 0 - -# is there a header line that identifies the columns? -header = yes - -# is there a row that specifies the order of columns in the image? -# - if so, this must be the first line of the header -# - if the line exists (col_order_row=yes), employ the use_col_order_row to toggle whether it is used -col_order_row = no -use_col_order_row = no - -# is there a row that specifies the size of columns in the image? -# - if so, this must be the next line of the header -# - if the line exists (col_size_row=yes), employ the use_col_size_row to toggle whether it is used -col_size_row = no -use_col_size_row = no - -# is there a row that specifies the color of each column segment in the image? -# - if so, this must be the next line of the header -# - if the line exists (col_color_row=yes), employ the use_col_color_row to toggle whether it is used -col_color_row = no -use_col_color_row = no - -# is there a column that specifies the order of rows in the image? -# - if so, this must be the first column -# - if the line exists (row_order_col=yes), employ the use_row_order_col to toggle whether it is used -row_order_col = no -use_row_order_col = no - -# is there a column that specifies the color of each row segment in the image? -# - if so, this must be the second column -# - if the line exists (row_color_col=yes), employ the use_row_color_col to toggle whether it is used -row_color_col = no -use_row_color_col = no - -# if you do not have a column/row that explicitly defines order -# of segments in the image, you can set this here. Use one (or more) of -# these values to specify how segments should be ordered. -# - row_major (row segments first, then column) -# - col_major (col segments first, then row) -# - ascii (asciibetic order) -# - row_size (total of rows for the segment - useful if the segment has both row and column contributions) -# - col_size (total of colums for the segment - useful if the segment has both row and column contributions) -# - row_to_col_ratio (ratio of total of rows to columns for the segment) -# - col_to_row_ratio (ratio of total of rows to columns for the segment) -# - size_asc (size, in ascending order) -# - size_desc (size, in descending order) - -#segment_order = row_to_col_ratio,size_desc # col_major,size_desc -#segment_order = size_desc -segment_order = row_major,size_desc -#segment_order = ascii -#segment_order = file:etc/order-by-table-remapped.txt -#segment_order = size_desc,row_to_col_ratio -segment_color_order = row_major,size_desc - -# values for segments can be normalized if the use_segment_normalization is set to yes -use_segment_normalization = no - -# the normalization function can be one of the following, and is applied to -# all values that correspond to the segment's label -# total - sum of cell values for the segment label (row and col) -# average - average of cell values for the segment label (row and col) -# row_total, row_average - sum or average for cell values for the segment row -# col_total, col_average - sum or average for cell values for the segment col -# row_size, col_size, total_size - based on the optional size column (see col_size_row and row_size_col above) -# VALUE - segments are scaled to a constant VALUE (e.g. 1000) -segment_normalization_function = 1000 - -# normalization can be performed by either altering the actual data values or -# by applying a visual scaling of the segments. When 'value' is used, the data -# is changed. When 'visual' is used, then a chromosomes_scale line is reported -# by this script which you must include in circos.conf for the scaling to be applied -segment_normalization_scheme = value - -################################################################ -# placement of cell ribbons on row/column segments -# -# for segments that share both column and row ribbons, the -# order of ribbon position can be adjusted with placement_order - -placement_order = row,col # col,row or row,col - -# within the row/column ribbon bundle for each segment, -# ribbon_bundle_order determines how the ribbons will be -# ordered -# - size - by value of the cell -# - ascii - sorted by destination label -# - native - sorted by order of destination segment - -ribbon_bundle_order = native # size, ascii, native - -# reverse the position of links in table/row segments? - -reverse_rows = no -reverse_columns = no - -# values for cells with the same row/column name can be treated -# independently. You can -# show - show these cells and not filter them at all -# hide - hide these cells from the image, but not resize the row/columns -# remove - entirely remove these cells from the data set (equivalent to setting cells to missing value) -intra_cell_handling = show - -# ribbon layering - order in which the ribbons are drawn on the image -# size_asc - ascending by ribbon size (small ribbons drawn first, therefore large ribbons will be at front) -# size_desc - descending by ribbon size (large ribbons drawn first, therefore small ribbons will be at front) - -ribbon_layer_order = size_asc - -# if both (A,B)=x and (B,A)=y cells exist, you can choose to have the ribbon -# ends sized variably so that ribbon at A has width x and at B has width y - -ribbon_variable = no -ribbon_variable_intra_collapse = yes - -################################################################ -# cell value mapping allows you to remap the cell values using -# any Perl expression that uses X as the cell value. For example, -# -# cell_remap_formula = log(X) -# = sqrt(X) -# = X/10 -# = X ? log(X) : 0 -# -# This remapping takes place before any filters or scaling is applied. Its effect -# is the same as remapping the cell values in the input file. - -use_cell_remap = no -cell_remap_formula = round(10*X) - -################################################################ -# scale your values with a power rule (useful if the range of values -# is very large) to -# - atten_large: attenuate large values and maintain visibility -# of ribbons corresponding to small values, or -# - atten_small: attenuate small values to increase visibility -# of ribbons corresponding to large values -# -# given a value, v, and a maximum, m -# -# atten_small: -# -# v_new = m * ( exp(scale_factor * v / m) - 1 ) / ( exp(scale_factor) - 1 ) -# -# atten_large: -# -# v_new = m * ( log(scale_factor * v ) ) / ( log(scale_factor * m ) ) -# -# essentially the values are remapped to a log-type scale -# with the range 0..m - -use_scaling = no -scaling_type = atten_large -scale_factor = 1 - -blank_means_missing = no -missing_cell_value = - - -################################################################ -# Value cutoffs for cell values and ribbon formatting. -# -# You can toggle the visibility of ribbons for cells outside -# a min/max range. You can define one or more of these cutoffs. -# The cutoffs are applied to unscaled cell values. - -#cell_min_value = 10 -#cell_min_percentile = 10 -#cell_max_value = 100 -#cell_max_percentile = 100 - -# For cell values that do not pass the min/max filters above, -# you can specify whether they are hidden or removed. If the -# parameter is not defined, "hide" will be assumed. -# hide - cell values won't be shown, but row/col will not be resized -# remove - entirely remove these cells from the data set (equivalent to setting cells to missing value) - -cutoff_cell_handling = hide - -# The color of ribbons is by default the color of the row segment from -# which they originate. The block below allows you to remap the color -# of the ribbons based on cell percentile values. There are two ways -# to remap colors -# -# - color_remap=yes, color_autoremap=no -# Uses <percentile> blocks to define the percentile values and associated -# color/stroke_color characteristics for ribbons. Percentile value defined -# in the block (e.g. <percentile 55>) is the max percentile value for -# cells associated with this block. -# - color_remap=yes, color_autoremap=yes -# Uses colors associated with each percentile window of size -# percentile_sampling for each cell - -<linkcolor> -color_source = row -percentile_source = larger -color_transparency = 1 -color_remap = yes -color_autoremap = no - -<percentile 50> -color = dgrey -transparency = 5 -</percentile> - -<percentile 60> -color = dgrey -transparency = 5 -</percentile> - -<percentile 70> -transparency = 1 -</percentile> - -<percentile 80> -transparency = 1 -</percentile> - -<percentile 90> -transparency = 1 -stroke_color = black -stroke_thickness = 1p -</percentile> - -<percentile 100> -transparency = 1 -stroke_color = black -stroke_thickness = 3p -</percentile> - -</linkcolor> - -<linkparam> -color = vdgrey -#stroke_color = black -#stroke_thickness = 1p -</linkparam> - -# If you are using color_autoremap=yes above, then -# define the percentile sampling window and -# the start/end HSV color values. Percentile window -# colors are interpolated between this HSV pair. -# -# HSV = (hue saturation value) -# hue=(0..360) saturation=(0..1) value=(0..1) - -percentile_sampling = 5 - -# count - percentile based on counts -# value - percentile based on value - -percentile_method = count - -# use all values or only unique values when -# calculating percentiles -percentile_unique_only = yes - -# use a function, f(X), to remap cell values when calculating percentiles -# for the purpose of color mapping. This allows you to apply a remapping to how -# colors are calculated, without actually changing the values. The remap -# applies only if percentile_method=value - -# percentile_remap = sqrt(X) - -# Which cell value set to use for percentile color mapping -# raw - original values -# filtered - values that pass min/max filters -# scaled - filtered values that have been scaled if use_scaling is set -percentile_data_domain = raw - -<colors> -h0 = 0 -s0 = 1 -v0 = 1 -h1 = 300 -s1 = 1 -v1 = 1 -</colors> - -# You can control the color and stroke of ribbons for each -# quartile (q1, q2, q3, q4). Any values defined here will -# overwrite colors determined by remapping. -# -# For example, if you have a lot of cells and wish to attenuate -# the visibility of ribbons associated with small values, you can -# set cell_q1_color=vvlgrey,cell_q1_nostroke=yes to fade the -# ribbons into the background. - -#cell_q1_color = vvlgrey -#cell_q2_color = vlgrey -#cell_q3_color = lgrey -#cell_q4_color = red -#cell_q1_nostroke = yes -#cell_q2_nostroke = yes -#cell_q3_nostroke = yes -#cell_q4_nostroke = yes - -# cell value multiplier, required when all data is small (e.g. <1), in which -# case set the multiplier to something like 1000 because Circos -# works only with integer scales - -data_mult = 1 - -################################################################ -# Segment labels can be optionally set to a size that is -# proportional to the size of the segment. Set min/max size -# values here. If this line is commented out, then the label -# size is determined by the circos.conf file used to draw the image - -#segment_label_size_range = 60,60 - -# progression controls how fast the label size changes from -# min to max (larger value of progression means values close to max -# are achieved for smaller segments) - -segment_label_size_progression = 4 - -segment_label_uppercase = no - -################################################################ -# Segment colors can be specified in the data file (in this -# case use row_color_col and col_color_row), otherwise colors -# are interpolated within an HSV range. Color interpolation can be -# done in two ways: based on segment index (interpolation steps through -# colors uniformly for each segment) and total size (interpolation -# steps through colors in proportion to segment size). - -<segment_colors> -interpolate_type = size # size or count -h0 = 0 -s0 = 0.8 -v0 = 0.9 -h1 = 300 -s1 = 0.8 -v1 = 0.9 -</segment_colors> - -################################################################ -# Shorten the labels of segments. Specify whether to do this -# with shorten_text=yes|no parameter and provide regular -# expressions in string_replace which define the text to -# replace. - -shorten_text = yes - -<string_replace> -IGH = -</string_replace> - -# exit on any error -strict_sanity = yes - -################################################################ -# if the segment_prefix is set, then rows and columns will be -# renamed to internal fields segment_prefix + DIGIT - -#segment_prefix = id -color_prefix = color - -################################################################ -# Delimiters - -# field delimiter regular expression -# if this is not defined, any whitespace will be considered a delimiter -field_delim = \s - -# collapse adjacent delimiters? -field_delim_collapse = yes - -# remove any leading space in the input file -# by default, this is on - if you set this to "no", make sure that you don't have any leading spaces in your table! -strip_leading_space = yes - -# remove quotes and thousand separators - concatenate characters to remove -# -# e.g. to remove characters a b c set remove_cell_rx=abc -# e.g. to remove characters " ' , set remove_cell_rx="', -remove_cell_rx = "', - + +################################################################ +# +# This is a fairly complicated configuration file. Take your time in +# experimenting and adjust one thing at a time :) +# +################################################################ + +max_col_num = 200 +max_row_num = 200 + +# skip this many rows before reading in header and data +skip_rows = 0 + +# is there a header line that identifies the columns? +header = yes + +# is there a row that specifies the order of columns in the image? +# - if so, this must be the first line of the header +# - if the line exists (col_order_row=yes), employ the use_col_order_row to toggle whether it is used +col_order_row = no +use_col_order_row = no + +# is there a row that specifies the size of columns in the image? +# - if so, this must be the next line of the header +# - if the line exists (col_size_row=yes), employ the use_col_size_row to toggle whether it is used +col_size_row = no +use_col_size_row = no + +# is there a row that specifies the color of each column segment in the image? +# - if so, this must be the next line of the header +# - if the line exists (col_color_row=yes), employ the use_col_color_row to toggle whether it is used +col_color_row = no +use_col_color_row = no + +# is there a column that specifies the order of rows in the image? +# - if so, this must be the first column +# - if the line exists (row_order_col=yes), employ the use_row_order_col to toggle whether it is used +row_order_col = no +use_row_order_col = no + +# is there a column that specifies the color of each row segment in the image? +# - if so, this must be the second column +# - if the line exists (row_color_col=yes), employ the use_row_color_col to toggle whether it is used +row_color_col = no +use_row_color_col = no + +# if you do not have a column/row that explicitly defines order +# of segments in the image, you can set this here. Use one (or more) of +# these values to specify how segments should be ordered. +# - row_major (row segments first, then column) +# - col_major (col segments first, then row) +# - ascii (asciibetic order) +# - row_size (total of rows for the segment - useful if the segment has both row and column contributions) +# - col_size (total of colums for the segment - useful if the segment has both row and column contributions) +# - row_to_col_ratio (ratio of total of rows to columns for the segment) +# - col_to_row_ratio (ratio of total of rows to columns for the segment) +# - size_asc (size, in ascending order) +# - size_desc (size, in descending order) + +#segment_order = row_to_col_ratio,size_desc # col_major,size_desc +#segment_order = size_desc +segment_order = row_major,size_desc +#segment_order = ascii +#segment_order = file:etc/order-by-table-remapped.txt +#segment_order = size_desc,row_to_col_ratio +segment_color_order = row_major,size_desc + +# values for segments can be normalized if the use_segment_normalization is set to yes +use_segment_normalization = no + +# the normalization function can be one of the following, and is applied to +# all values that correspond to the segment's label +# total - sum of cell values for the segment label (row and col) +# average - average of cell values for the segment label (row and col) +# row_total, row_average - sum or average for cell values for the segment row +# col_total, col_average - sum or average for cell values for the segment col +# row_size, col_size, total_size - based on the optional size column (see col_size_row and row_size_col above) +# VALUE - segments are scaled to a constant VALUE (e.g. 1000) +segment_normalization_function = 1000 + +# normalization can be performed by either altering the actual data values or +# by applying a visual scaling of the segments. When 'value' is used, the data +# is changed. When 'visual' is used, then a chromosomes_scale line is reported +# by this script which you must include in circos.conf for the scaling to be applied +segment_normalization_scheme = value + +################################################################ +# placement of cell ribbons on row/column segments +# +# for segments that share both column and row ribbons, the +# order of ribbon position can be adjusted with placement_order + +placement_order = row,col # col,row or row,col + +# within the row/column ribbon bundle for each segment, +# ribbon_bundle_order determines how the ribbons will be +# ordered +# - size - by value of the cell +# - ascii - sorted by destination label +# - native - sorted by order of destination segment + +ribbon_bundle_order = native # size, ascii, native + +# reverse the position of links in table/row segments? + +reverse_rows = no +reverse_columns = no + +# values for cells with the same row/column name can be treated +# independently. You can +# show - show these cells and not filter them at all +# hide - hide these cells from the image, but not resize the row/columns +# remove - entirely remove these cells from the data set (equivalent to setting cells to missing value) +intra_cell_handling = show + +# ribbon layering - order in which the ribbons are drawn on the image +# size_asc - ascending by ribbon size (small ribbons drawn first, therefore large ribbons will be at front) +# size_desc - descending by ribbon size (large ribbons drawn first, therefore small ribbons will be at front) + +ribbon_layer_order = size_asc + +# if both (A,B)=x and (B,A)=y cells exist, you can choose to have the ribbon +# ends sized variably so that ribbon at A has width x and at B has width y + +ribbon_variable = no +ribbon_variable_intra_collapse = yes + +################################################################ +# cell value mapping allows you to remap the cell values using +# any Perl expression that uses X as the cell value. For example, +# +# cell_remap_formula = log(X) +# = sqrt(X) +# = X/10 +# = X ? log(X) : 0 +# +# This remapping takes place before any filters or scaling is applied. Its effect +# is the same as remapping the cell values in the input file. + +use_cell_remap = no +cell_remap_formula = round(10*X) + +################################################################ +# scale your values with a power rule (useful if the range of values +# is very large) to +# - atten_large: attenuate large values and maintain visibility +# of ribbons corresponding to small values, or +# - atten_small: attenuate small values to increase visibility +# of ribbons corresponding to large values +# +# given a value, v, and a maximum, m +# +# atten_small: +# +# v_new = m * ( exp(scale_factor * v / m) - 1 ) / ( exp(scale_factor) - 1 ) +# +# atten_large: +# +# v_new = m * ( log(scale_factor * v ) ) / ( log(scale_factor * m ) ) +# +# essentially the values are remapped to a log-type scale +# with the range 0..m + +use_scaling = no +scaling_type = atten_large +scale_factor = 1 + +blank_means_missing = no +missing_cell_value = - + +################################################################ +# Value cutoffs for cell values and ribbon formatting. +# +# You can toggle the visibility of ribbons for cells outside +# a min/max range. You can define one or more of these cutoffs. +# The cutoffs are applied to unscaled cell values. + +#cell_min_value = 10 +#cell_min_percentile = 10 +#cell_max_value = 100 +#cell_max_percentile = 100 + +# For cell values that do not pass the min/max filters above, +# you can specify whether they are hidden or removed. If the +# parameter is not defined, "hide" will be assumed. +# hide - cell values won't be shown, but row/col will not be resized +# remove - entirely remove these cells from the data set (equivalent to setting cells to missing value) + +cutoff_cell_handling = hide + +# The color of ribbons is by default the color of the row segment from +# which they originate. The block below allows you to remap the color +# of the ribbons based on cell percentile values. There are two ways +# to remap colors +# +# - color_remap=yes, color_autoremap=no +# Uses <percentile> blocks to define the percentile values and associated +# color/stroke_color characteristics for ribbons. Percentile value defined +# in the block (e.g. <percentile 55>) is the max percentile value for +# cells associated with this block. +# - color_remap=yes, color_autoremap=yes +# Uses colors associated with each percentile window of size +# percentile_sampling for each cell + +<linkcolor> +color_source = row +percentile_source = larger +color_transparency = 1 +color_remap = yes +color_autoremap = no + +<percentile 50> +color = dgrey +transparency = 5 +</percentile> + +<percentile 60> +color = dgrey +transparency = 5 +</percentile> + +<percentile 70> +transparency = 1 +</percentile> + +<percentile 80> +transparency = 1 +</percentile> + +<percentile 90> +transparency = 1 +stroke_color = black +stroke_thickness = 1p +</percentile> + +<percentile 100> +transparency = 1 +stroke_color = black +stroke_thickness = 3p +</percentile> + +</linkcolor> + +<linkparam> +color = vdgrey +#stroke_color = black +#stroke_thickness = 1p +</linkparam> + +# If you are using color_autoremap=yes above, then +# define the percentile sampling window and +# the start/end HSV color values. Percentile window +# colors are interpolated between this HSV pair. +# +# HSV = (hue saturation value) +# hue=(0..360) saturation=(0..1) value=(0..1) + +percentile_sampling = 5 + +# count - percentile based on counts +# value - percentile based on value + +percentile_method = count + +# use all values or only unique values when +# calculating percentiles +percentile_unique_only = yes + +# use a function, f(X), to remap cell values when calculating percentiles +# for the purpose of color mapping. This allows you to apply a remapping to how +# colors are calculated, without actually changing the values. The remap +# applies only if percentile_method=value + +# percentile_remap = sqrt(X) + +# Which cell value set to use for percentile color mapping +# raw - original values +# filtered - values that pass min/max filters +# scaled - filtered values that have been scaled if use_scaling is set +percentile_data_domain = raw + +<colors> +h0 = 0 +s0 = 1 +v0 = 1 +h1 = 300 +s1 = 1 +v1 = 1 +</colors> + +# You can control the color and stroke of ribbons for each +# quartile (q1, q2, q3, q4). Any values defined here will +# overwrite colors determined by remapping. +# +# For example, if you have a lot of cells and wish to attenuate +# the visibility of ribbons associated with small values, you can +# set cell_q1_color=vvlgrey,cell_q1_nostroke=yes to fade the +# ribbons into the background. + +#cell_q1_color = vvlgrey +#cell_q2_color = vlgrey +#cell_q3_color = lgrey +#cell_q4_color = red +#cell_q1_nostroke = yes +#cell_q2_nostroke = yes +#cell_q3_nostroke = yes +#cell_q4_nostroke = yes + +# cell value multiplier, required when all data is small (e.g. <1), in which +# case set the multiplier to something like 1000 because Circos +# works only with integer scales + +data_mult = 1 + +################################################################ +# Segment labels can be optionally set to a size that is +# proportional to the size of the segment. Set min/max size +# values here. If this line is commented out, then the label +# size is determined by the circos.conf file used to draw the image + +#segment_label_size_range = 60,60 + +# progression controls how fast the label size changes from +# min to max (larger value of progression means values close to max +# are achieved for smaller segments) + +segment_label_size_progression = 4 + +segment_label_uppercase = no + +################################################################ +# Segment colors can be specified in the data file (in this +# case use row_color_col and col_color_row), otherwise colors +# are interpolated within an HSV range. Color interpolation can be +# done in two ways: based on segment index (interpolation steps through +# colors uniformly for each segment) and total size (interpolation +# steps through colors in proportion to segment size). + +<segment_colors> +interpolate_type = size # size or count +h0 = 0 +s0 = 0.8 +v0 = 0.9 +h1 = 300 +s1 = 0.8 +v1 = 0.9 +</segment_colors> + +################################################################ +# Shorten the labels of segments. Specify whether to do this +# with shorten_text=yes|no parameter and provide regular +# expressions in string_replace which define the text to +# replace. + +shorten_text = yes + +<string_replace> +IGH = +</string_replace> + +# exit on any error +strict_sanity = yes + +################################################################ +# if the segment_prefix is set, then rows and columns will be +# renamed to internal fields segment_prefix + DIGIT + +#segment_prefix = id +color_prefix = color + +################################################################ +# Delimiters + +# field delimiter regular expression +# if this is not defined, any whitespace will be considered a delimiter +field_delim = \s + +# collapse adjacent delimiters? +field_delim_collapse = yes + +# remove any leading space in the input file +# by default, this is on - if you set this to "no", make sure that you don't have any leading spaces in your table! +strip_leading_space = yes + +# remove quotes and thousand separators - concatenate characters to remove +# +# e.g. to remove characters a b c set remove_cell_rx=abc +# e.g. to remove characters " ' , set remove_cell_rx="', +remove_cell_rx = "', +