CODEWITHSUNDEEP
pythonfor-loopmatplotlibplot
user8669
user8669

Reputation: 133

How would I iterate over a list of files and plot them as subplots on a single figure?

I'm trying to plot files onto 8 subplots for 2 figures. I am using a for loop and enumerate operator, along with axarray to do this. I am almost there with the last step (with axarray) but need guidance as to how to finish it. Here's my code:

'import matplotlib.pyplot as plt
import parse_gctoo
import glob
f, ax1 = plt.subplots()

def histo_plotter(file, plot_title, ax):
    # read in file as string
    GCT_object = parse_gctoo.parse(file)
    # for c in range(9):
    #     print type(GCT_object.data_df.iloc[0][c])
    # computing median of rows in data_df
    # gene_medians = GCT_object.data_df.quantile(q=0.5,axis=1)
    # plot_title = "Gene expression levels for {}".format(cell)
    if plot_title == "ZSPCQNORM":
        gene_means = GCT_object.data_df.mean(axis=1)
        #making histogram of means
        ax.hist(gene_means)
        plt.title("MeanGeneExpressionZSPCQNORM")
        plt.xlabel("MedianGeneExpression")
        plt.ylabel("Count")
    elif plot_title == "QNORM":
        gene_medians = GCT_object.data_df.median(axis=1)
        #making histogram of medians
        ax.hist(gene_medians)
        plt.title("MedianGeneExpressionQNORM")
        plt.xlabel("MedianGeneExpression")
        plt.ylabel("Count")
plt.show()
f.savefig("hist_example1.png")



# plt.ylim(-1, 1)
# plt.xlim(-1,1)

# histo_plotter("/Users/eibelman/Desktop/ZSCOREDATA-    CXA061_SKL_48H_X1_B29_ZSPCQNORM_n372x978.gct.txt", "ZSPCQNORM", ax1)
#     histo_plotter("/Users/eibelman/Desktop/NewLJP005_A375_24H_X2_B19_QNORM_n373x978.gct.txt", "QNORM", ax1)
#########



# Create list of x2 LJP005 cell line files

z_list = glob.glob("/Volumes/cmap_obelix/pod/custom/LJP/roast/LJP005_[A375, A549, BT20, HA1E, HC515, HEPG2, HS578T, HT29]*X2*/zs/*ZSPCQNORM*.gct")
q_list = glob.glob("/Volumes/cmap_obelix/pod/custom/LJP/roast/LJP005_[A375, A549, BT20, HA1E, HC515, HEPG2, HS578T, HT29]*_X2_*/*_QNORM_*.gct")



# for loop which allows plotting multiple files in a single figure

f, axarray = plt.subplots(2, 4)
for n, single_q in enumerate(q_list):
     # axarray = plt.subplot(len(q_list), 1, n+1)
     axarray = histo_plotter(n, "QNORM", ax1)
    # axarray[n].plot()
plt.show()

# f, axarray = plt.subplots(2, 4)
# for n, single_z in enumerate(z_list):
#     # ax = plt.subplot(len(z_list), 1, n+1)
#     histo_plotter(single_z, "ZSPCQNORM", ax1)'

Upvotes: 1

Views: 2173

Answers (2)

Israel Unterman
Israel Unterman

Reputation: 13520

First, it's suffice to call plt.figure() once at the beginning of the loop.

Second, you need to use subplot correctly. Here is the doc of the subplot function:

Typical call signature:

subplot(nrows, ncols, plot_number) Where nrows and ncols are used to notionally split the figure into nrows * ncols sub-axes, and plot_number is used to identify the particular subplot that this function is to create within the notional grid. plot_number starts at 1, increments across rows first and has a maximum of nrows * ncols.

EDIT

If you want a new figure for each file, then on each iteration you should call plt.figure() without arguments.

Upvotes: 1

heltonbiker
heltonbiker

Reputation: 27615

You can try this:

import matplotlib.pyplot as plt

plt.figure()

for n, single_q in enumerate(q_list):
    ax = plt.subplot(len(q_list), 1, n+1)
    GCT_object = parse_gctoo.parse(single_q)
    gene_medians = GCT_object.data_df.median(axis=1)
    plt.hist(gene_medians)
    # tweak title, labels, etc.

plt.show()

Explaining:

  • enumerate iterates over the items (s) while also returning their indices (n);
  • the function subplot(size, column, row) requires these parameters: size is the total amount of subplots in the figure, and row and column determine the position for the current plot. n+1 is necessary to put the plot in the correct position along the plot grid;
  • I edited the rest of the code with your own data

Upvotes: 1

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