I am trying to make subplots.
I call many columns from a dataframe, turn them into array and plot them.
I want to plot them in 4 rows, 2 columns. But I only get 1 column (you can check the image). What am I doing wrong?
Here is my code:
for column in df3: #I call the dataframe
data=df3[column].values #Turn it into an array
fig = plt.figure()
plt.subplot (4,2,1) #I want 4 rows and 2 columns
ax,_=plot_topomap(data, sensors_pos, cmap='viridis', vmin=0, vmax=100, show=False)
plt.title("KNN" + " " + column) #This is the title for each subplot
fig.colorbar(ax)
plt.show
There are several things which might cause problems in your code and it's hard to find a solution without knowing the complete code.
In your code you create several figures. However, you really want one single figure. So the figure needs to be creates outside the loop.
Then you want to create subplots, so in every loop step you need to tell matplotlib to which subplot it should plot. This can be done by ax = fig.add_subplot(4,2,n) where n is a number which you increase in every run of the loop.
Next you call plot_topomap. But how would plot_topomap know what to plot where? You need to tell it, by supplying the keyword argument axes = ax.
Finally try to set a colorbar, with the return image as argument to the axes ax.
Of course I cannot test the following code, but it might do what you want, in case I interpreted everything well.
n = 1
fig = plt.figure()
for column in df3: #I call the dataframe
data=df3[column].values #Turn it into an array
ax = fig.add_subplot(4,2,n) #I want 4 rows and 2 columns
im,_ = plot_topomap(data, sensors_pos, cmap='viridis', vmin=0, vmax=100, show=False, axes=ax)
ax.set_title("KNN" + " " + column) #This is the title for each subplot
fig.colorbar(im, ax=ax)
n+=1
Related
When making a plot with with
fig, ax = plt.subplots()
x=[1,2,3,4,5,6,7,8,9,10]
y=[1,2,3,4,5,6,7,8,9,10]
ax.plot(x,y)
plt.show()
matplotlib will determine the tick spacing/location and value of the tick. Is there are way to extract this automatic spacing/location AND the value? I want to do this so i can pass it to
set_xticks()
for my secondary axis (using twiny()) then use set_ticklabels() with a custom label. I realise I could use secondary axes giving both a forward and inverse function however providing an inverse function is not feasible for the goal of my code.
So in the image below, the ticks are only showing at 2,4,6,8,10 rather than all the values of x and I want to somehow extract these values and position so I can pass to set_xticks() and then change the tick labels (on a second x axis created with twiny).
UPDATE
When using the fix suggested it works well for the x axis. However, it does not work well for the y-axis. For the y-axis it seems to take the dataset values for the y ticks only. My code is:
ax4 = ax.twinx()
ax4.yaxis.set_ticks_position('left')
ax4.yaxis.set_label_position('left')
ax4.spines["left"].set_position(("axes", -0.10))
ax4.set_ylabel(self.y_2ndary_label, fontweight = 'bold')
Y = ax.get_yticks()
ax4.yaxis.set_ticks(Y)
ax4.yaxis.set_ticklabels( Y*Y )
ax4.set_ylim(ax.get_ylim())
fig.set_size_inches(8, 8)
plt.show()
but this gives me the following plot. The plot after is the original Y axis. This is not the case when I do this on the x-axis. Any ideas?
# From "get_xticks" Doc: The locations are not clipped to the current axis limits
# and hence may contain locations that are not visible in the output.
current_x_ticks = ax.get_xticks()
current_x_limits = ax.get_xlim()
ax.set_yticks(current_x_ticks) # Use this before "set_ylim"
ax.set_ylim(current_x_limits)
plt.show()
I'm trying to write a simple program that reads in a CSV with various datasets (all of the same length) and automatically plots them all (as a Pandas Dataframe scatter plot) on the same figure. My current code does this well, but all the marker colors are the same (blue). I'd like to figure out how to make a colormap so that in the future, if I have much larger data sets (let's say, 100+ different X-Y pairings), it will automatically color each series as it plots. Eventually, I would like for this to be a quick and easy method to run from the command line. I did not have luck reading the documentation or stack exchange, hopefully this is not a duplicate!
I've tried the recommendations from these posts:
1)Setting different color for each series in scatter plot on matplotlib
2)https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.plot.scatter.html
3) https://matplotlib.org/users/colormaps.html
However, the first one essentially grouped the data points according to their position on the x-axis and made those groups of data the same color (not what I want, each series of data is roughly a linearly increasing function). The second and third links seemed to have worked, but I don't like the colormap choices (e.g. "viridis", many colors are too similar and it's hard to distinguish data points).
This is a simplified version of my code so far (took out other lines that automatically named axes, etc. to make it easier to read). I've also removed any attempts I've made to specify a colormap, for more of a blank canvas feel:
''' Importing multiple scatter data and plotting '''
import pandas as pd
import matplotlib.pyplot as plt
### Data file path (please enter Dataframe however you like)
path = r'/Users/.../test_data.csv'
### Read in data CSV
data = pd.read_csv(path)
### List of headers
header_list = list(data)
### Set data type to float so modified data frame can be plotted
data = data.astype(float)
### X-axis limits
xmin = 1e-4;
xmax = 3e-3;
## Create subplots to be plotted together after loop
fig, ax = plt.subplots()
### Since there are multiple X-axes (every other column), this loop only plots every other x-y column pair
for i in range(len(header_list)):
if i % 2 == 0:
dfplot = data.plot.scatter(x = "{}".format(header_list[i]), y = "{}".format(header_list[i + 1]), ax=ax)
dfplot.set_xlim(xmin,xmax) # Setting limits on X axis
plot.show()
The dataset can be found in the google drive link below. Thanks for your help!
https://drive.google.com/drive/folders/1DSEs8D7lIDUW4NIPBl2qW2EZiZxslGyM?usp=sharing
I have a data set I filtered to the following (sample data):
Name Time l
1 1.129 1G-d
1 0.113 1G-a
1 3.374 1B-b
1 3.367 1B-c
1 3.374 1B-d
2 3.355 1B-e
2 3.361 1B-a
3 1.129 1G-a
I got this data after filtering the data frame and converting it to CSV file:
# Assigns the new data frame to "df" with the data from only three columns
header = ['Names','Time','l']
df = pd.DataFrame(df_2, columns = header)
# Sorts the data frame by column "Names" as integers
df.Names = df.Names.astype(int)
df = df.sort_values(by=['Names'])
# Changes the data to match format after converting it to int
df.Time=df.Time.astype(int)
df.Time = df.Time/1000
csv_file = df.to_csv(index=False, columns=header, sep=" " )
Now, I am trying to graph lines for each label column data/items with markers.
I want the column l as my line names (labels) - each as a new line, Time as my Y-axis values and Names as my X-axis values.
So, in this case, I would have 7 different lines in the graph with these labels: 1G-d, 1G-a, 1B-b, 1B-c, 1B-d, 1B-e, 1B-a.
I have done the following so far which is the additional settings, but I am not sure how to graph the lines.
plt.xlim(0, 60)
plt.ylim(0, 18)
plt.legend(loc='best')
plt.show()
I used sns.lineplot which comes with hue and I do not want to have name for the label box. Also, in that case, I cannot have the markers without adding new column for style.
I also tried ply.plot but in that case, I am not sure how to have more lines. I can only give x and y values which create only one line.
If there's any other source, please let me know below.
Thanks
The final graph I want to have is like the following but with markers:
You can apply a few tweaks to seaborn's lineplot. Using some created data since your sample isn't really long enough to demonstrate:
# Create data
np.random.seed(2019)
categories = ['1G-d', '1G-a', '1B-b', '1B-c', '1B-d', '1B-e', '1B-a']
df = pd.DataFrame({'Name':np.repeat(range(1,11), 10),
'Time':np.random.randn(100).cumsum(),
'l':np.random.choice(categories, 100)
})
# Plot
sns.lineplot(data=df, x='Name', y='Time', hue='l', style='l', dashes=False,
markers=True, ci=None, err_style=None)
# Temporarily removing limits based on sample data
#plt.xlim(0, 60)
#plt.ylim(0, 18)
# Remove seaborn legend title & set new title (if desired)
ax = plt.gca()
handles, labels = ax.get_legend_handles_labels()
ax.legend(handles=handles[1:], labels=labels[1:], title='New Title', loc='best')
plt.show()
To apply markers, you have to specify a style variable. This can be the same as hue.
You likely want to remove dashes, ci, and err_style
To remove the seaborn legend title, you can get the handles and labels, then re-add the legend without the first handle and label. You can also specify the location here and set a new title if desired (or just remove title=... for no title).
Edits per comments:
Filtering your data to only a subset of level categories can be done fairly easily via:
categories = ['1G-d', '1G-a', '1B-b', '1B-c', '1B-d', '1B-e', '1B-a']
df = df.loc[df['l'].isin(categories)]
markers=True will fail if there are too many levels. If you are only interested in marking points for aesthetic purposes, you can simply multiply a single marker by the number of categories you are interested in (which you have already created to filter your data to categories of interest): markers='o'*len(categories).
Alternatively, you can specify a custom dictionary to pass to the markers argument:
points = ['o', '*', 'v', '^']
mult = len(categories) // len(points) + (len(categories) % len(points) > 0)
markers = {key:value for (key, value)
in zip(categories, points * mult)}
This will return a dictionary of category-point combinations, cycling over the marker points specified until each item in categories has a point style.
My data-frame contains the following column headers: subject, Group, MASQ_GDA, MASQ_AA, MASQ_GDD, MASQ_AD
I was successfully able to plot one of them using a bar plot with the following specifications:
bar_plot = sns.barplot(x="Group", y='MASQ_GDA', units="subject", ci = 68, hue="Group", data=demo_masq)
However, I am attempting to create several of such bar plot side by side. Might anyone know how I can accomplish this, for each plot to contain the remaining 3 variables (MASQ_AA, MASQ_GDD, MASQ_AD). Here is an example of what I am trying to achieve.
If you look in the documentation for sns.barplot(), you will see that the function accepts a parameter ax= allowing you to tell seaborn which Axes object to use to plot the result
ax : matplotlib Axes, optional
Axes object to draw the plot onto, otherwise uses the current Axes.
Therefore, the simple way to obtain the desired output is to create the Axes beforehand, and then calling sns.barplot() with the corresponding ax parameter
fig, axs = plt.subplots(1,4) # create 4 subplots on 1 row
for ax,col in zip(axs,["MASQ_GDA", "MASQ_AA", "MASQ_GDD", "MASQ_AD"]):
sns.barplot(x="Group", y=col, units="subject", ci = 68, hue="Group", data=demo_masq, ax=ax) # <- notice ax= argument
Another option, and maybe an option that is more in line with the philosophy of seaborn is to use a FacetGrid. This would allow you to automatically create the required number of subplots depending on the number of categories in your dataset. However, it requires to reshape your dataframe so that the content of your MASQ_* columns are on a single column, with a new column showing what category each value corresponds to.
I have a dataset with 80 variables. I am interested in creating a function that will automate the creation of a 20 X 4 GridSpec in Matplotlib. Each subplot would either contain a histogram or a barplot for each of the 80 variables in the data. As a first step, I successfully created two functions (I call them 'counts' and 'histogram') that contain the layout of the plot that I want. Both of them work when tested on individual variables. As a next step, I attempted to create a function that would take the column names, loop through a conditional to test whether the data type is an object or otherwise and call the right function based on the datatype as a new subplot. Here is the code that I have so far:
Creates list of coordinates we will need for subplot specification:
A = np.arange(21)
B = np.arange(4)
coords = []
for i in A:
for j in B:
coords.append([A[i], B[j]])
#Create the gridspec and layout the figure
import matplotlib.gridspec as gridspec
fig = plt.figure(figsize=(12,6))
gs = gridspec.GridSpec(2,4)
#Function that relies on what we've done above:
def grid(cols=['MSZoning', 'LotFrontage', 'LotArea', 'Street', 'Alley']):
for i in cols:
for vals in coords:
if str(train[i].dtype) == 'object':
plt.subplot('gs'+str(vals))
counts(cols)
else:
plt.subplot('gs'+str(vals))
histogram(cols)
When attempted, this code returns an error:
ValueError: Single argument to subplot must be a 3-digit integer
For purposes of helping you visualize, what I am hoping to achieve, I attach the screen shot below, which was produced by the line by line coding (with my created helper functions) I am trying to avoid:
Can anyone help me figure out where I am going wrong? I would appreciate any advice. Thank you!
The line plt.subplot('gs'+str(vals)) cannot work; which is also what the error tells you.
As can be seen from the matplotlib GridSpec tutorial, it needs to be
ax = plt.subplot(gs[0, 0])
So in your case you may use the values from the list as
ax = plt.subplot(gs[vals[0], vals[1]])
Mind that you also need to make sure that the coords list must have the n*m elements, if the gridspec is defined as gs = gridspec.GridSpec(n,m).