Bar plots¶

In [1]:

import sys

import matplotlib as mpl
import matplotlib.pyplot as plt
import plotly.express as px
import seaborn as sns

sys.path.append("..")

import arcadia_pycolor as apc

apc.mpl.setup()
apc.plotly.setup()

import sys import matplotlib as mpl import matplotlib.pyplot as plt import plotly.express as px import seaborn as sns sys.path.append("..") import arcadia_pycolor as apc apc.mpl.setup() apc.plotly.setup()

In [2]:

num_reads = [
    1_500_000,
    1_200_000,
    1_000_000,
    400_000,
    1_000_000,
    1_700_000,
    1_300_000,
    600_000,
    1_200_000,
    1_500_000,
    1_600_000,
    300_000,
    900_000,
    1_700_000,
    800_000,
]

sample_id = [
    "AL 4M",
    "EL 2W",
    "EL 4W",
    "EL 4W WGA",
    "EL 12W",
    "OM 2W",
    "OM 4W",
    "OM 4W WGA",
    "OM 8W",
    "WH 1M",
    "WH 2M",
    "WH 2M WGA",
    "WH 4M",
    "WH 2M Hous",
    "WI 3W",
]

error = [
    100000,
    80000,
    70000,
    30000,
    70000,
    120000,
    90000,
    40000,
    80000,
    100000,
    110000,
    20000,
    60000,
    120000,
    50000,
]

num_reads = [ 1_500_000, 1_200_000, 1_000_000, 400_000, 1_000_000, 1_700_000, 1_300_000, 600_000, 1_200_000, 1_500_000, 1_600_000, 300_000, 900_000, 1_700_000, 800_000, ] sample_id = [ "AL 4M", "EL 2W", "EL 4W", "EL 4W WGA", "EL 12W", "OM 2W", "OM 4W", "OM 4W WGA", "OM 8W", "WH 1M", "WH 2M", "WH 2M WGA", "WH 4M", "WH 2M Hous", "WI 3W", ] error = [ 100000, 80000, 70000, 30000, 70000, 120000, 90000, 40000, 80000, 100000, 110000, 20000, 60000, 120000, 50000, ]

1. Vertical bar chart using Matplotlib¶

In [3]:

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained")

sample_id_formatted = [i.replace(" ", "\n") for i in sample_id]
plt.bar(sample_id_formatted, num_reads, color=apc.aster)

apc.mpl.style_plot(ax, monospaced_axes="y")
apc.mpl.set_xaxis_categorical()

# Use this to format the y-axis with commas.
ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ",")))  # type: ignore

# Remove this if you don't want error bars.
plt.errorbar(sample_id_formatted, num_reads, yerr=error, fmt="none", color=apc.crow)

plt.ylabel("Number of reads")
plt.xlabel("Sample")
plt.show()

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained") sample_id_formatted = [i.replace(" ", "\n") for i in sample_id] plt.bar(sample_id_formatted, num_reads, color=apc.aster) apc.mpl.style_plot(ax, monospaced_axes="y") apc.mpl.set_xaxis_categorical() # Use this to format the y-axis with commas. ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ","))) # type: ignore # Remove this if you don't want error bars. plt.errorbar(sample_id_formatted, num_reads, yerr=error, fmt="none", color=apc.crow) plt.ylabel("Number of reads") plt.xlabel("Sample") plt.show()

2. Horizontal bar chart using Matplotlib¶

In [4]:

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("half_square"), layout="constrained")
plt.barh(sample_id, num_reads, color=apc.aster)

apc.mpl.style_plot(ax, monospaced_axes="x")
apc.mpl.set_yaxis_categorical()

ax.get_xaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ",")))  # type: ignore
plt.xticks(rotation=30, ha="right")

# Remove this if you don't want error bars.
plt.errorbar(num_reads, sample_id, xerr=error, fmt="none", color=apc.crow)

plt.xlabel("Number of reads")
plt.ylabel("Sample")
plt.show()

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("half_square"), layout="constrained") plt.barh(sample_id, num_reads, color=apc.aster) apc.mpl.style_plot(ax, monospaced_axes="x") apc.mpl.set_yaxis_categorical() ax.get_xaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ","))) # type: ignore plt.xticks(rotation=30, ha="right") # Remove this if you don't want error bars. plt.errorbar(num_reads, sample_id, xerr=error, fmt="none", color=apc.crow) plt.xlabel("Number of reads") plt.ylabel("Sample") plt.show()

3. Vertical bar chart using Seaborn¶

In [5]:

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained")
sns.barplot(
    x=sample_id_formatted,
    y=num_reads,
    color=apc.aster,
    saturation=1,  # Seaborn by default desaturates the colors. This prevents that.
)

apc.mpl.style_plot(ax, monospaced_axes="y")
apc.mpl.set_xaxis_categorical()

ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ",")))  # type: ignore

plt.ylabel("Number of reads")
plt.xlabel("Sample")
plt.show()

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained") sns.barplot( x=sample_id_formatted, y=num_reads, color=apc.aster, saturation=1, # Seaborn by default desaturates the colors. This prevents that. ) apc.mpl.style_plot(ax, monospaced_axes="y") apc.mpl.set_xaxis_categorical() ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ","))) # type: ignore plt.ylabel("Number of reads") plt.xlabel("Sample") plt.show()

4. Horizontal bar chart using Seaborn¶

In [6]:

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("half_square"), layout="constrained")
sns.barplot(
    y=sample_id,
    x=num_reads,
    color=apc.aster,
    saturation=1,  # Seaborn by default desaturates the colors. This prevents that.
)

apc.mpl.style_plot(ax, monospaced_axes="x")
apc.mpl.set_yaxis_categorical()

ax.get_xaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ",")))  # type: ignore

plt.xticks(rotation=30, ha="right")

plt.xlabel("Number of reads")
plt.ylabel("Sample")
plt.show()

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("half_square"), layout="constrained") sns.barplot( y=sample_id, x=num_reads, color=apc.aster, saturation=1, # Seaborn by default desaturates the colors. This prevents that. ) apc.mpl.style_plot(ax, monospaced_axes="x") apc.mpl.set_yaxis_categorical() ax.get_xaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ","))) # type: ignore plt.xticks(rotation=30, ha="right") plt.xlabel("Number of reads") plt.ylabel("Sample") plt.show()

5. Vertical bar chart using Plotly¶

In [7]:

fig = px.bar(x=sample_id, y=num_reads, error_y=error)
fig.update_layout(
    xaxis_title="Sample",
    yaxis_title="Number of reads",
    showlegend=False,
)
fig.update_traces(
    marker_color=apc.aster,
    error_y_color=apc.crow,
    error_y_thickness=1.5,
    error_y_width=0,
)

apc.plotly.style_plot(fig, categorical_axes="x", monospaced_axes="y")
apc.plotly.add_commas_to_axis_tick_labels(fig)
apc.plotly.set_figure_dimensions(fig, "full_wide")

fig.show()

fig = px.bar(x=sample_id, y=num_reads, error_y=error) fig.update_layout( xaxis_title="Sample", yaxis_title="Number of reads", showlegend=False, ) fig.update_traces( marker_color=apc.aster, error_y_color=apc.crow, error_y_thickness=1.5, error_y_width=0, ) apc.plotly.style_plot(fig, categorical_axes="x", monospaced_axes="y") apc.plotly.add_commas_to_axis_tick_labels(fig) apc.plotly.set_figure_dimensions(fig, "full_wide") fig.show()

6. Horizontal bar chart using Plotly¶

In [8]:

fig = px.bar(x=num_reads, y=sample_id, error_x=error)
fig.update_layout(
    xaxis_title="Number of reads",
    yaxis_title="Sample",
    showlegend=False,
)
fig.update_traces(
    marker_color=apc.aster,
    error_x_color=apc.crow,
    error_x_thickness=1.5,
    error_x_width=0,
)

apc.plotly.style_plot(fig, categorical_axes="y", monospaced_axes="x")
apc.plotly.add_commas_to_axis_tick_labels(fig)
apc.plotly.set_figure_dimensions(fig, "half_square")

fig.show()

fig = px.bar(x=num_reads, y=sample_id, error_x=error) fig.update_layout( xaxis_title="Number of reads", yaxis_title="Sample", showlegend=False, ) fig.update_traces( marker_color=apc.aster, error_x_color=apc.crow, error_x_thickness=1.5, error_x_width=0, ) apc.plotly.style_plot(fig, categorical_axes="y", monospaced_axes="x") apc.plotly.add_commas_to_axis_tick_labels(fig) apc.plotly.set_figure_dimensions(fig, "half_square") fig.show()

7. Bar chart with colored categories using Matplotlib¶

In [9]:

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained")

color_labels = [idx.split(" ")[0] for idx in sample_id]
color_dict = dict(zip(set(color_labels), [apc.aster, apc.aegean, apc.amber, apc.seaweed, apc.rose]))

colors = [dict(color_dict)[i] for i in color_labels]

sample_id_formatted = [i.replace(" ", "\n") for i in sample_id]
plt.bar(sample_id_formatted, num_reads, color=colors)

apc.mpl.style_plot(ax, monospaced_axes="y")
apc.mpl.set_xaxis_categorical()

ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ",")))  # type: ignore

plt.ylabel("Number of reads")
plt.xlabel("Sample")
plt.show()

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained") color_labels = [idx.split(" ")[0] for idx in sample_id] color_dict = dict(zip(set(color_labels), [apc.aster, apc.aegean, apc.amber, apc.seaweed, apc.rose])) colors = [dict(color_dict)[i] for i in color_labels] sample_id_formatted = [i.replace(" ", "\n") for i in sample_id] plt.bar(sample_id_formatted, num_reads, color=colors) apc.mpl.style_plot(ax, monospaced_axes="y") apc.mpl.set_xaxis_categorical() ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ","))) # type: ignore plt.ylabel("Number of reads") plt.xlabel("Sample") plt.show()

8. Bar chart with colored categories using Seaborn¶

In [10]:

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained")

color_labels = [idx.split(" ")[0] for idx in sample_id]
color_dict = dict(zip(set(color_labels), [apc.aster, apc.aegean, apc.amber, apc.seaweed, apc.rose]))

sns.barplot(
    x=sample_id_formatted,
    y=num_reads,
    hue=color_labels,
    palette=color_dict,
    saturation=1,  # Seaborn by default desaturates the colors. This prevents that.
)

apc.mpl.style_plot(ax, monospaced_axes="y")
apc.mpl.set_xaxis_categorical()

ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ",")))  # type: ignore

plt.ylabel("Number of reads")
plt.xlabel("Sample")

legend = ax.get_legend()
legend.set_title("ID")

legend.set_bbox_to_anchor((1.06, 1))

plt.show()

fig, ax = plt.subplots(figsize=apc.mpl.get_figure_dimensions("full_wide"), layout="constrained") color_labels = [idx.split(" ")[0] for idx in sample_id] color_dict = dict(zip(set(color_labels), [apc.aster, apc.aegean, apc.amber, apc.seaweed, apc.rose])) sns.barplot( x=sample_id_formatted, y=num_reads, hue=color_labels, palette=color_dict, saturation=1, # Seaborn by default desaturates the colors. This prevents that. ) apc.mpl.style_plot(ax, monospaced_axes="y") apc.mpl.set_xaxis_categorical() ax.get_yaxis().set_major_formatter(mpl.ticker.FuncFormatter(lambda x, _: format(int(x), ","))) # type: ignore plt.ylabel("Number of reads") plt.xlabel("Sample") legend = ax.get_legend() legend.set_title("ID") legend.set_bbox_to_anchor((1.06, 1)) plt.show()

9. Bar chart with colored categories using Plotly¶

In [11]:

color_labels = [idx.split(" ")[0] for idx in sample_id]
color_dict = {
    label: color
    for label, color in zip(
        set(color_labels), [apc.aster, apc.aegean, apc.amber, apc.seaweed, apc.rose]
    )
}

fig = px.bar(
    x=sample_id,
    y=num_reads,
    color=color_labels,
    color_discrete_map=color_dict,
    title=None,
)

fig.update_layout(
    xaxis_title="Sample",
    yaxis_title="Number of reads",
    legend=dict(title="ID"),
)

apc.plotly.style_plot(fig, categorical_axes="x", monospaced_axes="y")
apc.plotly.style_legend(fig)
apc.plotly.add_commas_to_axis_tick_labels(fig)
apc.plotly.set_figure_dimensions(fig, "full_wide")

fig.show()

color_labels = [idx.split(" ")[0] for idx in sample_id] color_dict = { label: color for label, color in zip( set(color_labels), [apc.aster, apc.aegean, apc.amber, apc.seaweed, apc.rose] ) } fig = px.bar( x=sample_id, y=num_reads, color=color_labels, color_discrete_map=color_dict, title=None, ) fig.update_layout( xaxis_title="Sample", yaxis_title="Number of reads", legend=dict(title="ID"), ) apc.plotly.style_plot(fig, categorical_axes="x", monospaced_axes="y") apc.plotly.style_legend(fig) apc.plotly.add_commas_to_axis_tick_labels(fig) apc.plotly.set_figure_dimensions(fig, "full_wide") fig.show()