colorschemes

Color schemes.

dmslogo.colorschemes.AA_CHARGE = {'A': '#000000', 'C': '#000000', 'D': '#0000FF', 'E': '#0000FF', 'F': '#000000', 'G': '#000000', 'H': '#FF0000', 'I': '#000000', 'K': '#FF0000', 'L': '#000000', 'M': '#000000', 'N': '#000000', 'P': '#000000', 'Q': '#000000', 'R': '#FF0000', 'S': '#000000', 'T': '#000000', 'V': '#000000', 'W': '#000000', 'Y': '#000000'}

color amino acids by charge

dmslogo.colorschemes.AA_FUNCTIONAL_GROUP = {'A': '#f76ab4', 'C': '#ff7f00', 'D': '#e41a1c', 'E': '#e41a1c', 'F': '#84380b', 'G': '#f76ab4', 'H': '#3c58e5', 'I': '#12ab0d', 'K': '#3c58e5', 'L': '#12ab0d', 'M': '#12ab0d', 'N': '#972aa8', 'P': '#12ab0d', 'Q': '#972aa8', 'R': '#3c58e5', 'S': '#ff7f00', 'T': '#ff7f00', 'V': '#12ab0d', 'W': '#84380b', 'Y': '#84380b'}

color amino acids by functional group

dmslogo.colorschemes.CBBPALETTE = ['#000000', '#E69F00', '#56B4E9', '#009E73', '#F0E442', '#0072B2', '#D55E00', '#CC79A7']

color-blind safe palette with black, from http://bconnelly.net/2013/10/creating-colorblind-friendly-figures

dmslogo.colorschemes.CBPALETTE = ['#999999', '#E69F00', '#56B4E9', '#009E73', '#F0E442', '#0072B2', '#D55E00', '#CC79A7']

color-blind safe palette with gray, from http://bconnelly.net/2013/10/creating-colorblind-friendly-figures

class dmslogo.colorschemes.ValueToColorMap(minvalue, maxvalue, cmap='viridis')

Bases: object

Map numerical values to color gradient.

Args:

minvalue (float)

Color map starts at this value.

maxvalue (float)

Color map ends at this value.

cmap (str or matplotlib.colors.Colormap)

Name of matplotlib colormap, or an actual Colormap object. You can also use the wider set of color maps from palettable, such as by providing palettable.cmocean.sequential.Dense_20.mpl_colormap.

Attributes:

cmap (matplotlib.colors.Colormap)

Color map.

minvalue (float)

Color map starts at this value.

maxvalue (float)

Color map ends at this value.

Make a data frame with some values, and two color maps (one with default ‘viridis’ and another with ‘cividis’) covering value range in data frame:

>>> import pandas as pd
>>> from dmslogo.colorschemes import ValueToColorMap
>>>
>>> df = pd.DataFrame({'value': [0, 1, 2, 1, 3, 0]})
>>> map1 = ValueToColorMap(df['value'].min(),
...                        df['value'].max())
>>> map2 = ValueToColorMap(df['value'].min(),
...                        df['value'].max(),
...                        cmap='cividis')

Map values to colors using ValueToColorMap.val_to_color():

>>> df = (df
...       .assign(color=lambda x: x['value'].map(map1.val_to_color),
...               color2=lambda x: x['value'].map(map2.val_to_color),
...               )
...       )
>>> df
   value    color   color2
0      0  #440154  #00224d
1      1  #30678d  #575d6d
2      2  #35b778  #a59b73
3      1  #30678d  #575d6d
4      3  #fde724  #fde737
5      0  #440154  #00224d

Draw scale bars:

>>> fig1, ax1 = map1.scale_bar(orientation='horizontal',
...                          label='viridis scale')

(png, hires.png, pdf)

>>> fig2, ax2 = map2.scale_bar(orientation='vertical',
...                          label='cividis scale')

(png, hires.png, pdf)

>>> fig2, ax2 = map2.scale_bar(orientation='vertical',
...                          label='cividis scale (alpha 0.3)',
...                          alpha=0.3)

(png, hires.png, pdf)

scale_bar(*, orientation='vertical', ax=None, label=None, axisfontscale=1, low_high_ticks_only=False, alpha=1)

Draw a scale bar for the value-to-color map.

Args:

orientation ({‘horizontal’, ‘vertical’})

Direction that scale bar drawn is drawn.

ax (None or matplotlib.axes.Axes)

If specified, draw scale bar on this axis. Otherwise create new axes.

label (None or str)

Label for scale bar.

axisfontscale (float)

Scale font size by this much.

low_high_ticks_only (bool)

Rather than showing numerical ticks, indicate low and high.

alpha (float)

Transparency of scale bar colors.

Returns:

(matplotlib.figure.Figure, matplotlib.axes.Axes), figure and axis on which the color bar is drawn.

val_to_color(values, *, return_color_as='rgb_hex_code')

Map numerical values between minvalue and maxvalue to colors.

Args:

values (number or array-like of numbers)

Values to map to colors

return_color_as ({‘rgb_hex_code’, ‘rgb_triple’})

Return color as RGB hex code (e.g., ‘#FF0000’) or triple of numbers (e.g., [255, 0, 0]).

Returns:

Either str or length-3 arrays depending on return_color_as. If values is single value, return single value; otherwise array.