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mavis.illustrate.scatter

class mavis.illustrate.scatter.ScatterPlot

holds settings that will go into matplotlib after conversion using the mapping system

mavis.illustrate.scatter.ScatterPlot.__init__()

def __init__(
    self,
    points,
    y_axis_label,
    ymax=None,
    ymin=None,
    xmin=None,
    xmax=None,
    hmarkers=None,
    height=100,
    point_radius=2,
    title='',
    yticks=None,
    colors=None,
    density=1,
    ymax_color='#FF0000',
):

Args

  • points
  • y_axis_label
  • ymax
  • ymin
  • xmin
  • xmax
  • hmarkers
  • height
  • point_radius
  • title
  • yticks
  • colors
  • density
  • ymax_color

mavis.illustrate.scatter.bam_to_scatter()

pull data from a bam file to set up a scatter plot of the pileup

def bam_to_scatter(
    bam_file,
    chrom,
    start,
    end,
    density,
    strand=None,
    axis_name=None,
    ymax=None,
    min_mapping_quality=0,
    ymax_color='#FF0000',
):

Args

  • bam_file (str): path to the bam file
  • chrom (str): chromosome name
  • start (int): genomic start position for the plot
  • end (int): genomic end position for the plot
  • density
  • strand (STRAND): expected strand
  • axis_name (str): axis name
  • ymax (int): maximum value to plot the y axis
  • min_mapping_quality (int): minimum mapping quality for reads to be considered in the plot
  • ymax_color

Returns

  • ScatterPlot: the scatter plot representing the bam pileup

mavis.illustrate.scatter.draw_scatter()

given a xmapping, draw the scatter plot svg group

def draw_scatter(ds, canvas, plot, xmapping, log=DEVNULL):

Args

  • ds (DiagramSettings): the settings/constants to use for building the svg
  • canvas (svgwrite.canvas): the svgwrite object used to create new svg elements

  • plot (ScatterPlot): the plot to be drawn

  • log