Package nelpy.plotting examples¶
Here we will look at some of the different plot types and utilities in the nelpy.plotting module.
Let's start with the required imports.
In [1]:
Copied!
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as np
import nelpy as nel # recommended import for nelpy
import nelpy.plotting as npl # recommended import for the nelpy plotting library
%matplotlib inline
import matplotlib.gridspec as gridspec import matplotlib.pyplot as plt import numpy as np import nelpy as nel # recommended import for nelpy import nelpy.plotting as npl # recommended import for the nelpy plotting library %matplotlib inline
Flexible scalebar implementation¶
Nelpy includes a powerful and flexible scalebar implementation based on an excellent gist by Dan Meliza (see https://gist.github.com/dmeliza/3251476). Nelpy extends the basic functionality in a number of ways, and formats the scalebar labels correctly.
In [ ]:
Copied!
fig = plt.figure(1, figsize=(12, 4))
ax = fig.add_subplot(241)
npl.add_scalebar(ax=ax, sizex=0.25, labelx="10 cm")
ax.set_title("horizontal")
ax = fig.add_subplot(242)
npl.add_scalebar(ax=ax, sizey=0.15, labely="5 cm")
ax.set_title("vertical")
ax = fig.add_subplot(243)
npl.add_scalebar(ax=ax, sizex=0.15, sizey=0.3, labelx="5 ms", labely="100 $\mu$V")
ax.set_title("both")
ax = fig.add_subplot(244)
npl.add_scalebar(
ax=ax, sizex=0.15, sizey=0.3, labelx="5 ms", labely="100 $\mu$V", sep=16
)
ax.set_title("sep labels from bars")
ax = fig.add_subplot(245)
npl.add_scalebar(
ax=ax, sizex=0.15, sizey=0.3, labelx="5 ms", labely="100 $\mu$V", pad=2
)
ax.set_title("padding")
ax = fig.add_subplot(246)
npl.add_scalebar(ax=ax, sizex=0.25, labelx="10 cm", fc="red", ec="deepskyblue", loc=2)
ax.set_title("change colors; loc=2")
ax = fig.add_subplot(247)
npl.add_scalebar(
ax=ax,
sizex=0.4,
labelx="10 cm",
fc="red",
ec="deepskyblue",
lw=5,
fontsize=16,
sep=5,
)
ax.set_title("linewidth and fontsize")
ax = fig.add_subplot(248)
npl.add_scalebar(
ax=ax, sizex=0.25, labelx="10 cm", matchy=True, fc="gray", ec="gray", hidey=False
)
ax.set_title("autoscale; show axis")
fig = plt.figure(1, figsize=(12, 4)) ax = fig.add_subplot(241) npl.add_scalebar(ax=ax, sizex=0.25, labelx="10 cm") ax.set_title("horizontal") ax = fig.add_subplot(242) npl.add_scalebar(ax=ax, sizey=0.15, labely="5 cm") ax.set_title("vertical") ax = fig.add_subplot(243) npl.add_scalebar(ax=ax, sizex=0.15, sizey=0.3, labelx="5 ms", labely="100 $\mu$V") ax.set_title("both") ax = fig.add_subplot(244) npl.add_scalebar( ax=ax, sizex=0.15, sizey=0.3, labelx="5 ms", labely="100 $\mu$V", sep=16 ) ax.set_title("sep labels from bars") ax = fig.add_subplot(245) npl.add_scalebar( ax=ax, sizex=0.15, sizey=0.3, labelx="5 ms", labely="100 $\mu$V", pad=2 ) ax.set_title("padding") ax = fig.add_subplot(246) npl.add_scalebar(ax=ax, sizex=0.25, labelx="10 cm", fc="red", ec="deepskyblue", loc=2) ax.set_title("change colors; loc=2") ax = fig.add_subplot(247) npl.add_scalebar( ax=ax, sizex=0.4, labelx="10 cm", fc="red", ec="deepskyblue", lw=5, fontsize=16, sep=5, ) ax.set_title("linewidth and fontsize") ax = fig.add_subplot(248) npl.add_scalebar( ax=ax, sizex=0.25, labelx="10 cm", matchy=True, fc="gray", ec="gray", hidey=False ) ax.set_title("autoscale; show axis")
Out[ ]:
<matplotlib.text.Text at 0x9b242b0>
The options for the location (loc) parameter are listed below:
'upper right' : 1,
'upper left' : 2,
'lower left' : 3,
'lower right' : 4, default
'right' : 5,
'center left' : 6,
'center right' : 7,
'lower center' : 8,
'upper center' : 9,
'center' : 10.Plotting spike rasters¶
In [ ]:
Copied!
stdata1 = [1, 2, 4, 5, 6, 10, 20]
stdata2 = [3, 4, 4.5, 5, 5.5, 19]
stdata3 = [5, 12, 14, 15, 16, 18, 22, 23, 24]
stdata4 = [5, 12, 14, 15, 16, 18, 23, 25, 32]
ep1 = nel.EpochArray([[0.8, 2.8], [4.5, 5]], fs=1)
# ep1 = EpochArray([[0.8, 2.8]], fs=1)
sta1 = nel.SpikeTrainArray(
[stdata1, stdata2, stdata3, stdata4, stdata1 + stdata4], fs=5
)
sta2 = nel.SpikeTrainArray(
[stdata1, stdata2, stdata3, stdata4, stdata1 + stdata4], support=ep1, fs=5
)
sta3 = nel.SpikeTrainArray([stdata1, stdata3], fs=5, unit_ids=[10, 13])
npl.raster(sta1, cmap=plt.cm.Blues)
npl.raster(sta2, cmap=plt.cm.gray)
npl.raster(sta3, color="orange", lw=4)
# npl.raster(sta3, cmap=plt.cm.gray, lw=3) # this will result in an error due to color indexing
npl.raster(sta2.support)
stdata1 = [1, 2, 4, 5, 6, 10, 20] stdata2 = [3, 4, 4.5, 5, 5.5, 19] stdata3 = [5, 12, 14, 15, 16, 18, 22, 23, 24] stdata4 = [5, 12, 14, 15, 16, 18, 23, 25, 32] ep1 = nel.EpochArray([[0.8, 2.8], [4.5, 5]], fs=1) # ep1 = EpochArray([[0.8, 2.8]], fs=1) sta1 = nel.SpikeTrainArray( [stdata1, stdata2, stdata3, stdata4, stdata1 + stdata4], fs=5 ) sta2 = nel.SpikeTrainArray( [stdata1, stdata2, stdata3, stdata4, stdata1 + stdata4], support=ep1, fs=5 ) sta3 = nel.SpikeTrainArray([stdata1, stdata3], fs=5, unit_ids=[10, 13]) npl.raster(sta1, cmap=plt.cm.Blues) npl.raster(sta2, cmap=plt.cm.gray) npl.raster(sta3, color="orange", lw=4) # npl.raster(sta3, cmap=plt.cm.gray, lw=3) # this will result in an error due to color indexing npl.raster(sta2.support)
unit labels from object: ['1', '2', '3', '4', '5'] unit labels from object: ['1', '2', '3', '4', '5'] unit labels from object: ['10', '13']
C:\Anaconda3\lib\site-packages\nelpydev\objects.py:2066: UserWarning: ignoring spikes outside of spiketrain support 'ignoring spikes outside of spiketrain support')
Out[ ]:
<matplotlib.axes._subplots.AxesSubplot at 0x88b32e8>
EpochArray intersections¶
In [ ]:
Copied!
ep1 = nel.EpochArray([1200, 1400], fs=1)
ep2 = nel.EpochArray([[1150, 1210], [1220, 1240], [1380, 1420], [1500, 1550]], fs=1)
fig = plt.figure(figsize=(12, 4))
gs = gridspec.GridSpec(2, 3, hspace=0.3)
ax1 = plt.subplot(gs[0])
npl.epoch_plot(ax=ax1, epochs=ep1, height=1)
ax1.set_xlim([1100, 1600])
ax1.set_title("ep1")
ax2 = plt.subplot(gs[1])
npl.epoch_plot(ax=ax2, epochs=ep2, height=1)
ax2.set_xlim([1100, 1600])
ax2.set_title("ep2")
ax3 = plt.subplot(gs[2])
npl.epoch_plot(ax=ax3, epochs=ep1[ep2], height=1)
ax3.set_xlim([1100, 1600])
ax3.set_title("ep1[ep2]")
ax4 = plt.subplot(gs[3])
npl.epoch_plot(ax=ax4, epochs=ep2[ep1], height=1)
ax4.set_xlim([1100, 1600])
ax4.set_title("ep2[ep1]")
ax5 = plt.subplot(gs[4])
npl.epoch_plot(ax=ax5, epochs=ep2.intersect(ep1, boundaries=True), height=1)
ax5.set_xlim([1100, 1600])
ax5.set_title("ep2.intersect(ep1)")
ax6 = plt.subplot(gs[5])
npl.epoch_plot(ax=ax6, epochs=ep1.intersect(ep2), height=1)
ax6.set_xlim([1100, 1600])
ax6.set_title("ep1.intersect(ep2)")
print("==== ep1 ====")
for ep in ep1:
print(ep)
print("==== ep2 ====")
for ep in ep2:
print(ep)
print("== ep2[ep1] =")
for ep in ep2[ep1]:
print(ep)
ep1 = nel.EpochArray([1200, 1400], fs=1) ep2 = nel.EpochArray([[1150, 1210], [1220, 1240], [1380, 1420], [1500, 1550]], fs=1) fig = plt.figure(figsize=(12, 4)) gs = gridspec.GridSpec(2, 3, hspace=0.3) ax1 = plt.subplot(gs[0]) npl.epoch_plot(ax=ax1, epochs=ep1, height=1) ax1.set_xlim([1100, 1600]) ax1.set_title("ep1") ax2 = plt.subplot(gs[1]) npl.epoch_plot(ax=ax2, epochs=ep2, height=1) ax2.set_xlim([1100, 1600]) ax2.set_title("ep2") ax3 = plt.subplot(gs[2]) npl.epoch_plot(ax=ax3, epochs=ep1[ep2], height=1) ax3.set_xlim([1100, 1600]) ax3.set_title("ep1[ep2]") ax4 = plt.subplot(gs[3]) npl.epoch_plot(ax=ax4, epochs=ep2[ep1], height=1) ax4.set_xlim([1100, 1600]) ax4.set_title("ep2[ep1]") ax5 = plt.subplot(gs[4]) npl.epoch_plot(ax=ax5, epochs=ep2.intersect(ep1, boundaries=True), height=1) ax5.set_xlim([1100, 1600]) ax5.set_title("ep2.intersect(ep1)") ax6 = plt.subplot(gs[5]) npl.epoch_plot(ax=ax6, epochs=ep1.intersect(ep2), height=1) ax6.set_xlim([1100, 1600]) ax6.set_title("ep1.intersect(ep2)") print("==== ep1 ====") for ep in ep1: print(ep) print("==== ep2 ====") for ep in ep2: print(ep) print("== ep2[ep1] =") for ep in ep2[ep1]: print(ep)
C:\Anaconda3\lib\site-packages\nelpydev\objects.py:528: UserWarning: meta data is not available
warnings.warn("meta data is not available")
==== ep1 ==== <EpochArray: 1 epoch> totaling 200.0 seconds ==== ep2 ==== <EpochArray: 1 epoch> totaling 60.0 seconds <EpochArray: 1 epoch> totaling 20.0 seconds <EpochArray: 1 epoch> totaling 40.0 seconds <EpochArray: 1 epoch> totaling 50.0 seconds == ep2[ep1] = <EpochArray: 1 epoch> totaling 10.0 seconds <EpochArray: 1 epoch> totaling 20.0 seconds <EpochArray: 1 epoch> totaling 20.0 seconds
C:\Anaconda3\lib\site-packages\nelpydev\objects.py:528: UserWarning: meta data is not available
warnings.warn("meta data is not available")
Multiple traces with no axis borders¶
In [ ]:
Copied!
n_traces = 30
fig, axes = plt.subplots(n_traces, 1, figsize=(3.5, 3))
for ax in axes:
data = np.random.randn(40)
ax.plot(data, color="k")
npl.utils.clear_left_right(*axes)
npl.utils.clear_top_bottom(*axes)
npl.scalebar.add_scalebar(
ax=axes[0], sizex=5, sizey=10, labely="10 Hz", labelx="500 ms", pad=1, loc=3
)
n_traces = 30 fig, axes = plt.subplots(n_traces, 1, figsize=(3.5, 3)) for ax in axes: data = np.random.randn(40) ax.plot(data, color="k") npl.utils.clear_left_right(*axes) npl.utils.clear_top_bottom(*axes) npl.scalebar.add_scalebar( ax=axes[0], sizex=5, sizey=10, labely="10 Hz", labelx="500 ms", pad=1, loc=3 )
Out[ ]:
<matplotlib.axes._subplots.AxesSubplot at 0x7f8460dcb630>
