# How to make arrow plots that visualize change

After a quick Google search, I realize that there may not be such a thing as an arrow plot and I may have made up the term. Regardless of whether it's an actual type of plot or not, I've found them useful in visualizing changes in some variable across individuals and this post describes how to make them in Python.

I first made the plot when I was trying to illustrate the variability in individuals' responses to neurostimulation. At the group level, our lab found that stimulating the right inferior frontal gyrus with repetitive Transcranial Magnetic Stimulation made participants more cautious to identify previously studied faces during a recognition memory experiment. We only observed this pattern in one condition and I wanted to visualize how participants' decision criteria changed before vs. after TMS in each condition. Normally I would use a strip plot with different colored points for before vs. after stimulation, but I thought replacing the points with an arrow pointed in the direction of the change would make for a simpler, more intuitive plot. Here's what the arrow plots looked like in the poster:

The dots in the arrow plots denote the participants' decision criteria before stimulation and the tip of the arrow heads denote their decision criteria after stimulation.

I use these plots often to visualize changes in participants' behaviors before vs. after neurostimulation, but they can be used in any situation where you need to illustrate how some variable changed among different entities. For example, you could use them to show how population changed among different US states, how mean salaries changed among different occupations, or how stock prices changed among different corporations.

You can view and download the Jupyter notebook I made to create the plots here

First, we'll import libraries, define some formatting, and create some data to plot.

```import pandas as pd
import numpy as np

import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib.colors
%matplotlib inline

#set font size of labels on matplotlib plots
plt.rc('font', size=16)

#set style of plots
sns.set_style('white')
```
```n = 30 #number of subjects

#create dataframe
data = pd.DataFrame(columns=['subject','before','after','change'], index=range(n))
data.loc[:,'subject'] = range(n)
data.loc[:,'before'] = np.random.normal(0, 0.5, n)
data.loc[:,'after'] = np.random.normal(0.25, 0.5, n)
data.loc[:,'change'] = data['after'] - data['before']

data.head()
```

### ARROW PLOT 1: BEFORE vs. AFTER VALUES

This is the same arrow plot I made for the ICB poster. The arrows start at the "before score" and end at the "after score." The participants are sorted according to how much their scores changed.

```#sort individuals by amount of change, from largest to smallest
data = data.sort_values(by='change', ascending=False) \
.reset_index(drop=True)

#initialize a plot
ax = plt.figure(figsize=(5,10))

#add start points
ax = sns.stripplot(data=data,
x='before',
y='subject',
orient='h',
order=data['subject'],
size=10,
color='black')

#define arrows
arrow_starts = data['before'].values
arrow_lengths = data['after'].values - arrow_starts

#add arrows to plot
for i, subject in enumerate(data['subject']):
ax.arrow(arrow_starts[i],        #x start point
i,                      #y start point
arrow_lengths[i],       #change in x
0,                      #change in y
head_width=0.6,         #arrow head width
head_length=0.2,        #arrow head length
width=0.2,              #arrow stem width
fc='black',             #arrow fill color
ec='black')             #arrow edge color

#format plot
ax.set_title('Scores before vs. after stimulation')   #add title
ax.axvline(x=0, color='0.9', ls='--', lw=2, zorder=0) #add line at x=0
ax.grid(axis='y', color='0.9')                        #add a light grid
ax.set_xlim(-2,2)                                     #set x axis limits
ax.set_xlabel('score')                                #label the x axis
ax.set_ylabel('participant')                          #label the y axis
sns.despine(left=True, bottom=True)                   #remove axes
```

### ARROW PLOT 2: NORMALIZED CHANGES

This plot visualizes the change in scores, and not the scores themselves. It's effective if you want to emphasize the magnitude of change, and not the actual start points or end points. It looks cleaner, but it also conveys less information.

```#sort individuals by amount of change, from largest to smallest
data = data.sort_values(by='change', ascending=True) \
.reset_index(drop=True)

#initialize a plot
fig, ax = plt.subplots(figsize=(5,10))
ax.set_xlim(-1.5,1.5)
ax.set_ylim(-1,n)
ax.set_yticks(range(n))
ax.set_yticklabels(data['subject'])

#define arrows
arrow_starts = np.repeat(0,n)
arrow_lengths = data['change'].values

#add arrows to plot
for i, subject in enumerate(data['subject']):
ax.arrow(arrow_starts[i],        #x start point
i,                      #y start point
arrow_lengths[i],       #change in x
0,                      #change in y
head_width=0.6,         #arrow head width
head_length=0.2,        #arrow head length
width=0.2,              #arrow stem width
fc='black',             #arrow fill color
ec='black')             #arrow edge color

#format plot
ax.set_title('Changes in scores')                     #add title
ax.axvline(x=0, color='0.9', ls='--', lw=2, zorder=0) #add line at x=0
ax.grid(axis='y', color='0.9')                        #add a light grid
ax.set_xlim(-2,2)                                     #set x axis limits
ax.set_xlabel('change')                               #label the x axis
ax.set_ylabel('participant')                          #label the y axis
sns.despine(left=True, bottom=True)                   #remove axes
```

### ARROW PLOT 3: COLOR-CODED ARROWS

You can also color-code the arrows to illustrate positive or negative change:

```#sort individuals by amount of change, from largest to smallest
data = data.sort_values(by='change', ascending=True) \
.reset_index(drop=True)

#initialize a plot
fig, ax = plt.subplots(figsize=(5,10))   #create figure
ax.set_xlim(-2,2)                        #set x axis limits
ax.set_ylim(-1,n)                        #set y axis limits
ax.set_yticks(range(n))                  #add 0-n ticks
ax.set_yticklabels(data['subject'])      #add y tick labels

#define arrows
arrow_starts = np.repeat(0,n)
arrow_lengths = data['change'].values

#add arrows to plot
for i, subject in enumerate(data['subject']):

if arrow_lengths[i] > 0:
arrow_color = '#347768'
elif arrow_lengths[i] < 0:
arrow_color = '#6B273D'
else:
arrow_color = 'black'

ax.arrow(arrow_starts[i],        #x start point
i,                      #y start point
arrow_lengths[i],       #change in x
0,                      #change in y
head_width=0.6,         #arrow head width
head_length=0.2,        #arrow head length
width=0.2,              #arrow stem width
fc=arrow_color,             #arrow fill color
ec=arrow_color)             #arrow edge color

#format plot
ax.set_title('Changes in scores')                     #add title
ax.axvline(x=0, color='0.9', ls='--', lw=2, zorder=0) #add line at x=0
ax.grid(axis='y', color='0.9')                        #add a light grid
ax.set_xlim(-2,2)                                     #set x axis limits
ax.set_xlabel('change')                               #label the x axis
ax.set_ylabel('participant')                          #label the y axis
sns.despine(left=True, bottom=True)                   #remove axes
```

# 7 ways to label a cluster plot in Python

This tutorial shows you 7 different ways to label a scatter plot with different groups (or clusters) of data points. I made the plots using the Python packages matplotlib and seaborn, but you could reproduce them in any software. These labeling methods are useful to represent the results of clustering algorithms, such as k-means clustering, or when your data is divided up into groups that tend to cluster together.

Here's a sneak peek of some of the plots:

You can access the Juypter notebook I used to create the plots here. I also embedded the code below.

First, we need to import a few libraries and define some basic formatting:

```import pandas as pd
import numpy as np

import seaborn as sns
import matplotlib.pyplot as plt
%matplotlib inline

#set font size of labels on matplotlib plots
plt.rc('font', size=16)

#set style of plots
sns.set_style('white')

#define a custom palette
customPalette = ['#630C3A', '#39C8C6', '#D3500C', '#FFB139']
sns.set_palette(customPalette)
sns.palplot(customPalette)
```

### CREATE LABELED GROUPS OF DATA

Next, we need to generate some data to plot. I defined four groups (A, B, C, and D) and specified their center points. For each label, I sampled nx2 data points from a gaussian distribution centered at the mean of the group and with a standard deviation of 0.5.

To make these plots, each datapoint needs to be assigned a label. If your data isn't labeled, you can use a clustering algorithm to create artificial groups.

```#number of points per group
n = 50

#define group labels and their centers
groups = {'A': (2,2),
'B': (3,4),
'C': (4,4),
'D': (4,1)}

#create labeled x and y data
data = pd.DataFrame(index=range(n*len(groups)), columns=['x','y','label'])
for i, group in enumerate(groups.keys()):
#randomly select n datapoints from a gaussian distrbution
data.loc[i*n:((i+1)*n)-1,['x','y']] = np.random.normal(groups[group],
[0.5,0.5],
[n,2])
#add group labels
data.loc[i*n:((i+1)*n)-1,['label']] = group

data.head()
```

### STYLE 1: STANDARD LEGEND

Seaborn makes it incredibly easy to generate a nice looking labeled scatter plot. This style works well if your data points are labeled, but don't really form clusters, or if your labels are long.

```#plot data with seaborn
facet = sns.lmplot(data=data, x='x', y='y', hue='label',
fit_reg=False, legend=True, legend_out=True)
```

### STYLE 2: COLOR-CODED LEGEND

This is a slightly fancier version of style 1 where the text labels in the legend are also color-coded. I like using this option when I have longer labels. When I'm going for a minimal look, I'll drop the colored bullet points in the legend and only keep the colored text.

```#plot data with seaborn (don't add a legend yet)
facet = sns.lmplot(data=data, x='x', y='y', hue='label',
fit_reg=False, legend=False)

#add a legend
leg = facet.ax.legend(bbox_to_anchor=[1, 0.75],
title="label", fancybox=True)
#change colors of labels
for i, text in enumerate(leg.get_texts()):
plt.setp(text, color = customPalette[i])

```

### STYLE 3: COLOR-CODED TITLE

This option can work really well in some contexts, but poorly in others. It probably isn't a good option if you have a lot of group labels or the group labels are very long. However, if you have only 2 or 3 labels, it can make for a clean and stylish option. I would use this type of labeling in a presentation or in a blog post, but I probably wouldn't use in more formal contexts like an academic paper.

```#plot data with seaborn
facet = sns.lmplot(data=data, x='x', y='y', hue='label',
fit_reg=False, legend=False)

#define padding -- higher numbers will move title rightward
pad = 4.5

#define separation between cluster labels
sep = 0.3

#define y position of title
y = 5.6

#add beginning of title in black
facet.ax.text(pad, y, 'Distributions of points in clusters:',
ha='right', va='bottom', color='black')

#add color-coded cluster labels
for i, label in enumerate(groups.keys()):
text = facet.ax.text(pad+((i+1)*sep), y, label,
ha='right', va='bottom',
color=customPalette[i])
```

### STYLE 4: LABELS NEXT TO CLUSTERS

This is my favorite style and the labeling scheme I use most often. I generally like to place labels next to the data instead of in a legend. The only draw back of this labeling scheme is that you need to hard code where you want the labels to be positioned.

```#define labels and where they should go
labels = {'A': (1.25,1),
'B': (2.25,4.5),
'C': (4.75,3.5),
'D': (4.75,1.5)}

#create a new figure
plt.figure(figsize=(5,5))

#loop through labels and plot each cluster
for i, label in enumerate(groups.keys()):

#add data points
plt.scatter(x=data.loc[data['label']==label, 'x'],
y=data.loc[data['label']==label,'y'],
color=customPalette[i],
alpha=0.7)

#add label
plt.annotate(label,
labels[label],
horizontalalignment='center',
verticalalignment='center',
size=20, weight='bold',
color=customPalette[i])
```

### STYLE 5: LABELS CENTERED ON CLUSTER MEANS

This style is advantageous if you care more about where the cluster means are than the locations of the individual points. I made the points more transparent to improve the visibility of the labels.

```#create a new figure
plt.figure(figsize=(5,5))

#loop through labels and plot each cluster
for i, label in enumerate(groups.keys()):

#add data points
plt.scatter(x=data.loc[data['label']==label, 'x'],
y=data.loc[data['label']==label,'y'],
color=customPalette[i],
alpha=0.20)

#add label
plt.annotate(label,
data.loc[data['label']==label,['x','y']].mean(),
horizontalalignment='center',
verticalalignment='center',
size=20, weight='bold',
color=customPalette[i])
```

### STYLE 6: LABELS CENTERED ON CLUSTER MEANS (2)

This style is similar to style 5, but relies on a different way to improve label visibility. Here, the background of the labels are color-coded and the text is white.

```#create a new figure
plt.figure(figsize=(5,5))

#loop through labels and plot each cluster
for i, label in enumerate(groups.keys()):

#add data points
plt.scatter(x=data.loc[data['label']==label, 'x'],
y=data.loc[data['label']==label,'y'],
color=customPalette[i],
alpha=1)

#add label
plt.annotate(label,
data.loc[data['label']==label,['x','y']].mean(),
horizontalalignment='center',
verticalalignment='center',
size=20, weight='bold',
color='white',
backgroundcolor=customPalette[i])
```

### STYLE 7: TEXT MARKERS

This style is a little bit odd, but it can be effective in some situations. This type of labeling scheme may be useful when there are few data points and the labels are very short.

```#create a new figure and set the x and y limits
fig, axes = plt.subplots(figsize=(5,5))
axes.set_xlim(0.5,5.5)
axes.set_ylim(-0.5,5.5)

#loop through labels and plot each cluster
for i, label in enumerate(groups.keys()):

#loop through data points and plot each point
for l, row in data.loc[data['label']==label,:].iterrows():

#add the data point as text
plt.annotate(row['label'],
(row['x'], row['y']),
horizontalalignment='center',
verticalalignment='center',
size=11,
color=customPalette[i])
```