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I was trying to get a figure from a Pandas dataframe. Apparently an easy job until I got into an unexpected problem I cannot get through : the plt.show() produces a figure showing only 20 lines of the 58 contained in the dataframe. Here is the code with output from the python3 interpreter:

print(df1) #1
         DDgun  mCSM   SDM  DeepDDG  DynaMut2
VARIANT                                      
G39C      -1.4 -0.56 -0.24    -0.75     -0.66
W63R      -0.6 -0.50  0.21    -0.23      0.42
L66P      -1.0 -0.68 -1.17    -0.92     -0.23
A67P      -0.3 -0.28 -0.67    -0.66     -0.19
E68K      -0.3  0.11 -0.04    -0.14      0.10
R70C      -0.7 -0.09 -0.31    -0.93      0.40
R70G      -0.9 -0.14 -0.03    -0.70     -0.26
R70H      -0.3 -0.58 -0.14    -0.62     -0.56
V71M      -0.5 -0.44 -0.66    -1.59     -0.75
E72A      -0.4 -0.40  0.23    -0.42     -0.28
R73P      -0.4  0.26  0.67    -0.59      0.30
G75D       0.0 -0.35  0.17     0.06     -0.46
S76C      -0.1 -0.23  0.71    -0.30     -0.32
V78G      -3.1 -2.05 -2.26    -2.72     -2.32
A80T      -0.9 -1.62 -1.78    -1.99     -1.80
W82G      -5.8 -3.62 -2.07    -4.79     -3.44
V89M      -1.2 -0.75 -2.13    -3.88     -0.59
S93P      -0.2 -0.12 -1.37    -1.99      0.13
G96D      -0.5 -0.62 -0.60    -2.21     -0.08
K97T       0.1 -0.42 -0.64    -0.50     -0.27
W99C      -2.1 -1.40  0.08    -2.01     -0.70
T101I      0.4  0.02 -0.33     0.13      0.38
G103S     -0.7 -1.26 -2.95    -1.97     -0.84
G108V      0.1 -0.38 -2.64    -1.38     -0.97
P114A     -0.4 -2.47  2.10    -2.13     -2.31
P114L      1.7 -3.03  0.62    -2.57     -0.96
P114S     -1.0 -1.00  3.11    -2.07     -3.05
A117D     -3.2 -2.83 -3.66    -5.70     -1.54
A117G     -2.4 -1.71 -2.21    -3.14     -1.92
A117V      0.8 -0.06 -1.14    -1.55     -0.32
Y119C     -3.1 -1.68 -1.59    -0.29     -1.68
L120F     -1.5 -1.49 -1.48    -1.41     -1.16
L120H     -4.2 -2.63 -1.82    -4.87     -0.74
E122D     -0.5 -1.06 -1.40    -1.04     -0.63
C123S     -0.1 -0.46 -1.17    -0.23      0.33
G124S     -0.5 -0.46 -1.17    -0.23     -0.43
G124V      0.1 -0.78 -2.68    -1.56     -1.08
S125F      1.1 -0.43 -2.29    -1.42     -1.12
L128F     -0.6 -1.10  0.52     0.39     -1.69
F129S     -2.1 -1.63 -0.78    -2.32     -2.22
D132A     -0.0 -2.45 -0.64    -2.32      0.04
A140T     -0.3 -0.17  1.18    -0.30     -0.99
L145Q     -1.9 -1.21 -2.54    -1.04     -1.67
Y155N     -4.8 -1.97 -1.76    -1.70     -2.19
V157F     -1.5 -2.34 -2.39    -4.32     -1.32
R170Q     -0.4 -1.32 -1.32    -3.19     -0.61
W296C     -1.1 -0.41 -0.25    -1.12      0.09
F303S     -2.0 -0.41 -0.10    -0.59     -0.44
P304L     -0.7 -1.03 -0.19    -0.83     -0.22
P318T     -1.2 -0.30 -0.58    -0.66     -0.36
P324L     -0.6 -0.73 -0.82    -1.70     -0.22
Y381C     -3.0 -0.28 -0.58    -1.00     -0.14
K463T      0.0 -1.23 -0.37    -1.55     -0.75
L488P     -3.7 -0.92 -0.16    -2.80     -0.85
P499L     -0.4 -1.09 -2.58    -4.06     -0.32
P499R     -0.9 -0.34  0.58    -0.97     -0.56
F512S     -3.5 -0.30  1.20    -1.01     -2.06
L520F     -0.6 -2.25 -0.83    -1.76     -0.66

ax=sns.heatmap(df1,cmap='rocket')

plt.show()

This is the picture I get:

enter image description here

Thanks in advance for your help.

Talha Tayyab
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Maurizio Cirilli
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    I don't know the best way to handle this. But, this is happening because you have too many rows you are trying to squeeze into the figure. The data is all being represented, it's just that the labels can't all be written out. You could try to reduce the font of the labels. Here is how I cheezed it: `fig, ax = plt.subplots(1, 1, figsize=(10, 30)); sns.heatmap(df1,cmap='rocket', ax=ax); plt.show()` – piRSquared Mar 31 '22 at 16:33

1 Answers1

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This seems reasonable. I manually added the y ticks AND the y tick labels. To improve the appearance, I used sns.set to adjust the size of the figure.

sns.set(rc = {'figure.figsize':(5, 20)})  # (width_inches, width_height)
ax = sns.heatmap(df1, cmap='rocket')
ax.set_yticks(np.arange(len(df1)) + .5)
ax.set_yticklabels(df1.index, fontsize=12)
plt.show()

enter image description here

tdy
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piRSquared
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  • After ax.set_yticklabels(df1.index, fontsize=12) got ValueError: The number of FixedLocator locations (20), usually from a call to set_ticks, does not match the number of ticklabels (58) – Maurizio Cirilli Mar 31 '22 at 17:09
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    That is why I used `ax.set_yticks` first so that I wouldn't get that error. – piRSquared Mar 31 '22 at 17:14
  • NB in matplotlib 3.5.0+, they've [added a `labels` param to `set_yticks`](https://stackoverflow.com/a/70272709/13138364) for this very reason. – tdy Apr 01 '22 at 05:26