Category

Plot


Usage

hifive 5c-heatmap [-h] [-b BINSIZE] [-t] [-r REGIONS] [-d {raw,fragment,distance,enrichment,expected}] [-a {compact,full}] [-y] [-x EXPBINSIZE] [-f MINOBS] [-g SEARCH] [-v] [-i IMAGE] [-p] [-l] [-n] [-k KEYWORDS] [-q] project output


Manual

-h, --help    Display the help message and command/subcommand options and arguments and exit.
-q, --quiet    Suppress all messages generated during HiFive processing.
-r, --re str    The name of the restriction enzyme.
-g, --genome str    The name of the genome.
-B, --bam FILES    A pair of BAM filenames separated by spaces corresponding to the two independently-mapped ends of a set of reads. Multiple file pairs may be passed by calling this argument more than once. This option is mutually exclusive with -C/–count.
-C, --count FILE    A tabular text file containing pairs of fragment primer names and their associated read count (see Loading 5C Data for more information). This option is mutually exclusive with -B/–bam.
-f, --min-interactions int    The minimum number of interactions with valid fragments to keep a fragment in the analysis. [20]
-m, --min-distance int    The minimum distance between fragment midpoints to include in calculating numbers of interactions for fragment filtering and (if called by 5c-normalization or 5c-complete) the minimum interaction distance included in learning correction parameter values. [0]
-x, --max-distance int    The maximum distance between fragment midpoints to include in calculating numbers of interactions for fragment filtering and (if called by 5c-normalization or 5c-complete) the maximum interaction distance included in learning correction parameter values. A value of zero indicates no maximum distance cutoff. [0]
-r, --regions str    A comma-separated list of region numbers to include fragments from when calculating correction parameter values. [all regions]
-o, --output FILE    An optional filename to save the updated HiFive project to, leaving the original unchanged. [None]
-o, --output FILES    A set of three filenames separated by spaces to save the newly-created HiFive fragment, dataset, and project files to. Mutually exclusive with -P/–prefix.
-P, --prefix str    A prefix for the output filenames. The file extensions .frags, .fcd, and .fcp will be used for the fragment, dataset, and project files, respectively. This option is mutually exclusive with -o/–output.
-b, --max-iterations int    The maximum number of iterations to run the learning process for. [1000]
-g, --min-change dec    The minimum allowable absolute gradient size to coninute learning process. [0.0005]
-p, --precalculate    Prior to beginning learning, set initial guesses for each correction value to be learned to the fragment’s mean difference between its log-counts and predicted distance-dependence signal.
-l, --learning-step dec    The scaling factor for decreasing learning rate by if step doesn’t meet Armijo criterion. [0.5]
    -e, --express-iterations int    The number of iterations to run the learning process for. [1000]
-d, --remove-distance    Calculate and subtract out the predicted distance-dependence signal from each log-count prior to learning correction parameters.
-w, --express-reads str    Which set reads to use for learning correction parameter values, cis, trans, or all. [cis]
-k, --logged    Use log-counts instead of counts for learning.
-z, --knight-ruiz    Use the Knight Ruiz matrix balancing algorithm instead of weighted matrix balancing. This option ignores ‘iterations’ and ‘logged’.
    -b, --binsize int    The width of bins (in basepairs) to partition data into. A value of zero indicates that each bin is to correspond with a single fragment. [10000]
-t, --trans    Calculate and include trans interactions in heatmaps.
-r, --regions str    A comma-separated list if region numbers to include in the heatmaps. [all regions]
-d, --datatype str    Type of data to produce for the heatmaps. Valid options are raw, fragment (only fragment corrections applied), distance (only distance-dependence signal removed), enrichment (both fragment correction and distance-dependence signal removed), and expected (only predicted signal). [fragment]
-a, --arraytype str    If data is unbinned, this option specifies whether the heatmaps should be full or compact. Full means that there is a row and column for every fragment, while compact means that rows are forward fragments only and columns are reverse fragments only. [full]
-y, --dynamically-bin    Dynamically bin heatmap.
-x, --expansion-binsize int    The size of bins, in base pairs, to group data into for expanding under-populated bins. [10000]
-f, --minobservations int    The minimum number of observed reads in a bin for it to be considered valid. [20]
-g, --search-distance int    The furthest distance from the bin minpoint to expand bounds. If set to zero, there is no limit on expansion distance. [0]
-v, --remove-failed    If a non-zero ‘search-distance’ is given, it is possible for a bin not to meet the ‘minobservations’ criteria before stopping looking. If this occurs and ‘remove-failed’ is set, the observed and expected values for that bin are zero.
    -c, --region int    The index of the region to pull data from.
-b, --binsize int    The width of bins (in basepairs) to partition data into. A value of zero indicates that each bin is to correspond with a single fragment.
-s, --start int    The first coordinate of the region to pull data from. None indicates the beginning of the region. [None]
-e, --stop int    The last coordinate + 1 of the region to pull data from. None indicates the end of the region. [None]
-y, --dynamically-bin    Dynamically bin heatmap.
-x, --expansion-binsize int    The size of bins, in base pairs, to group data into for expanding under-populated bins. [10000]
-f, --minobservations int    The minimum number of observed reads in a bin for it to be considered valid. [20]
-g, --search-distance int    The furthest distance from the bin minpoint to expand bounds. If set to zero, there is no limit on expansion distance. [0]
-v, --remove-failed    If a non-zero ‘search-distance’ is given, it is possible for a bin not to meet the ‘minobservations’ criteria before stopping looking. If this occurs and ‘remove-failed’ is set, the observed and expected values for that bin are zero.
-i, --image FILE    Generate an image from the region or regions for which heatmap data is being calculated. [None]
-p, --pdf    Format the image as a pdf. [None]
-r, --rotate    Rotate the image 45 degrees so the chromosome axis is horizontal and only plot the triangle above this axis. This option can only be used with a full arraytype.
-t, --ticks    Add coordinate ticks and labels to heatmap. This option can only be used if a pdf is requested.
-l, --legend    Add a color scale bar corresponding to interaction strength. This option can only be used if a pdf is requested.
-n, --names    Add region names to the plot. This option can only be used if a pdf is requested.
-k, --keyword str    Pass additional plotting options accepted by the plotting module. Arguments should be of the format KEYWORD=VALUE. This option can be passed multiple times. [None]


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