coalispr.count_analyze.panel_plotters¶

Module for organizing panes, based on samples and grouping, and plotting.

Attributes¶

logger

Classes¶

`PanelPlotter`	Create paneled figure to display grouped graphs (described by `fcie`).
`CountPanelPlotter`	Create paneled figure to display grouped library count graphs.
`Log2CountPanelPlotter`	Create paneled figure to display grouped library log2(count) graphs.
`LengthPanelPlotter`	Create paneled figure to display grouped length distribution graphs;
`BinPanelPlotter`	Create paneled figure to display grouped length distribution graphs;
`BrokenLengthPanelPlotter`	Create paneled figure to display grouped length graphs; each graph needs
`RegionCountPanelPlotter`	Create paneled figure to display grouped region count graphs.
`Log2RegionCountPanelPlotter`	Create paneled figure to display grouped library log2(count) graphs.

Module Contents¶

coalispr.count_analyze.panel_plotters.logger¶

class coalispr.count_analyze.panel_plotters.PanelPlotter(group, nams, lens, sampls, df, numbers, titles)¶

Create paneled figure to display grouped graphs (described by fcie).

group¶

Name of group of categories; data for each category is shown in a separate panel.

Type:: str

nams¶

List of group names in each group.

Type:: list

lens¶

Dict of group name vs number of samples in each group.

Type:: dict

sampls¶

Dict for group name vs members of group.

Type:: dict

df¶

Dataframe with data to display.

Type:: Pandas.DataFrame

numbers¶

List of column headers to use.

Type:: list

titels¶

Dictionary of figure titles: {‘legtitl’: ‘’,’suptitl’:’’, ‘wintitl’:’’}.

Type:: dict

dolegend¶

Flag to show legend.

Type:: bool

hfac¶

Height factor, determining vertical space for individual sample-lanes

Type:: float

gap¶

Space in gridspec lines for legend

Type:: int

xlabel¶

Label on x-axis describing what the displayed bars refer to.

Type:: str

ylabel¶

Label on y-axis describing sample data is displayed for.

Type:: str

savdir¶

Name of sub-directory to store saved figure in.

Type:: str

savedirect¶

Flag to save figure directly to file (to prevent distortion by resizing or scaling)

Type:: bool

figure¶

Type:: matplotlib.pyplot.figure

Returns:: Figure to be plotted or written to file.
Return type:: matplotlib.pyplot.figure

group¶

nams¶

lens¶

sampls¶

df¶

numbers¶

titles¶

dolegend = True¶

format_ax = None¶

hfac = 0.125¶

gap = 2¶

xlabel¶

ylabel¶

savdir = None¶

fig¶

plot_panels()¶

class coalispr.count_analyze.panel_plotters.CountPanelPlotter(group, nams, lens, sampls, df, numbers, titles)¶

Bases: PanelPlotter

Create paneled figure to display grouped library count graphs.

fcie¶

log2_ax = None¶

savdir = 'libcounts'¶

class coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter(group, nams, lens, sampls, df, numbers, titles)¶

Bases: CountPanelPlotter

Create paneled figure to display grouped library log2(count) graphs.

fcie¶

log2_ax = 'x'¶

savdir = 'libcounts'¶

class coalispr.count_analyze.panel_plotters.LengthPanelPlotter(group, nams, lens, sampls, df, numbers, titles)¶

Bases: PanelPlotter

Create paneled figure to display grouped length distribution graphs; each graph needs its own ax in a ‘multipane’ panel (therefore very similar idx-functions as in CountPanelPlotter()._build_panels, but with different handling, marked by # in margin).