BIOLOGIST J

evolutionary & developmental biology, bioinformatics, and other thoughts

seaborn棒形圖加計數值

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jasonbio

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目的：

  • 利用seaborn畫出棒形圖（barplot），比較不同物種的編碼基因（coding genes）數量
  • 在每根柱子上顯示計數值（count）

準備數據：

根據基因組數據庫（Ensembl release 104，NCBI）及基因組定序文獻，整理出以下脊椎動物的編碼基因數量：

物種物種
(英文)		學名基因組編碼基因數量參考資料
小鼠mouseMus musculusGRCm3922,468Ensembl[1], Genome Reference Consortium (GRC)[2]
人humanHomo sapiensGRCh38.p1320,442Ensembl[3], GRC[2]
家犬dogCanis lupus familiarisCanFam3.120,257Ensembl[4], Wang et al. Commun Biol (2021)[5]
家貓catFelis catusFelis_catus_9.019,588Ensembl[6], Buckley et al. PLoS Genet (2020)[7]
鴨嘴獸platypusOrnithorhynchus anatinusmOrnAna1.p.v117,418Ensembl[8], Zhou et al. Nature (2021)[9]
雞chickenGallus gallusGRCg6a16,878Ensembl[10], GRC[2]
鴿pigeonColumba liviaCliv_2.115,392NCBI[11], Holt et al. G3 (2018)[12]
鴯鶓emuDromaius novaehollandiaedroNov115,615Ensembl[13], Sackton et al. Science (2019)[14]
鱷魚crocodileCrocodylus porosusCpor_3.023,242NCBI[15], Ghosh et al. Genome Biol Evol (2020)[16]
鱉softshell turtlePelodiscus sinensisPelSin_1.018,189Ensembl[17], Wang et al. Nat Genet (2013)[18]
喙頭蜥tuataraSphenodon punctatusASM311381v117,648Ensembl[19], Gemmell et al. Nature (2020)[20]
蠑螈axolotlAmbystoma mexicanumAmbMex60DD23,251NCBI[21], Nowoshilow et al. Nature (2018)[22]
熱帶爪蟾western
clawed frog		Xenopus tropicalisXenopus_tropicalis_v9.119,987Ensembl[23], Xenbase[24]
肺魚lungfishNeoceratodus forsterineoFor_v331,120NCBI[25], Meyer et al. Nature (2021)[26]
腔棘魚coelacanthLatimeria chalumnaeLatCha119,569Ensembl[27], Amemiya et al. Nature (2013)[28]
斑馬魚zebrafishDanio rerioGRCz1125,592Ensembl[29], GRC[2]
河豚fuguTakifugu rubripesfTakRub1.221,411Ensembl[30]
海馬seahorseHippocampus comesH_comes_QL1_v120,852Ensembl[31], Lin et al. Nature (2016)[32]
鯊bamboo-sharkChiloscyllium punctatumCpunctatum_v1.034,038NCBI[33], Hara et al. Nat Ecol Evol (2018)[34]
盲鰻hagfishEptatretus burgeriEburgeri_3.216,513Ensembl[35], Yamaguchi et al. bioRxiv (2020)[36]
七鰓鰻lampreyPetromyzon marinusPmarinus_7.010,415Ensembl[37], Smith et al. Nat Genet (2013)[38]
dict_CodingGeneNumber = {
    'mouse': [22468, 'mammal'],
    'human': [20442, 'mammal'],
    'dog': [20257, 'mammal'],
    'cat': [19588, 'mammal'],
    'platypus': [17418, 'mammal'],
    'chicken': [16878, 'bird'],
    'pigeon': [15392, 'bird'],
    'emu': [15615, 'bird'],
    'crocodile': [23242, 'reptile'],
    'softshell turtle': [18189, 'reptile'],
    'tuatara': [17648, 'reptile'],
    'axolotl': [23251, 'amphibian'],
    'western clawed frog': [19987, 'amphibian'],
    'lungfish': [31120, 'lobe-finned fish'],
    'coelacanth': [19569, 'lobe-finned fish'],
    'zebrafish': [25592, 'ray-finned fish'],
    'fugu': [21411, 'ray-finned fish'],
    'seahorse': [20852, 'ray-finned fish'],
    'bambooshark': [34038, 'cartilaginous fish'],
    'hagfish': [16513, 'jawless fish'],
    'lamprey': [10415, 'jawless fish']
}

# 把dictionary轉換成dataframe
import pandas as pd
df = pd.DataFrame(data = dict_CodingGeneNumber, 
                  index = ['count_CodingGenes', 'group']).T

# 把dataframe轉換成seaborn作圖格式
df.reset_index(inplace = True)
df.columns = ['species'] + list(df.columns[1:])

df.head(8)

DataFrame首八行:

    species count_CodingGenes   group
0     mouse             22468  mammal
1     human             20442  mammal
2       dog             20257  mammal
3       cat             19588  mammal
4  platypus             17418  mammal
5   chicken             16878    bird
6    pigeon             15392    bird
7       emu             15615    bird

代碼：

剛剛發現在matplotlib新版本3.4中，可直接在棒上方標註記數值（若使用舊版本，則需先取得每根柱子在圖中的位置，再從而計算出標記計數值文字的位置，比較麻煩）。先更新作圖模組：

python3 -m pip install matplotlib==3.4.3
python3 -m pip install seaborn==0.11.2

利用seaborn畫出基礎圖：

sns.barplot(data = df,
            x = 'species', y = 'count_CodingGenes')

美化圖像：

  1. 改變圖像大小
  2. 柱子根據'group'列資訊填色
  3. 圖例放在主圖框之外
  4. 更改橫、縱軸文字方向、大小
  5. 更改字型
# Set figure size
plt.figure(figsize = (18,7.5))

# Plot barplot
ax = sns.barplot(data = df,
                 x = 'species', y = 'count_CodingGenes',
                 hue = 'group', dodge = False,
                 palette = 'Set3')

# Legend box outside the main frame
plt.legend(bbox_to_anchor = (1.05, 1), 
           loc = 'upper left',
           fontsize = 16)

# Rotate x-axis tick labels and change fontsize
plt.xticks(rotation=90, fontsize = 18)
plt.yticks(fontsize = 18)

# Rename axis labels
plt.xlabel('species', fontweight = 'bold', fontsize = 20)
plt.ylabel('number of coding genes', fontweight = 'bold', fontsize = 20)

# Set font
plt.rcParams["font.family"] = "Arial"

# Show plot
plt.tight_layout()
plt.show()

加上計數值[39]：

# Annotate counts
n_groups = len(df.group.unique())
for i in range(n_groups):
    ax.bar_label(ax.containers[i], fontsize = 14)

# 或者以下方法
# Annotate counts
for container in ax.containers:
    ax.bar_label(container, fontsize = 14)

註：如果只用ax.bar_label(ax.containers[0])，則只有第一組（最左方淺綠色柱子）被標記計數值。ax.containers中有八組數據。

完成圖：

參考資料及文獻
（All websites accessed on 2021-08-24）

  1. https://asia.ensembl.org/Mus_musculus/Info/Annotation.
  2. https://www.ncbi.nlm.nih.gov/grc.
  3. https://asia.ensembl.org/Homo_sapiens/Info/Annotation.
  4. https://asia.ensembl.org/Canis_lupus_familiaris/Info/Annotation.
  5. Wang, C. et al. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biology 4, 185 (2021).
  6. https://asia.ensembl.org/Felis_catus/Info/Annotation.
  7. Buckley, R. M. et al. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 16, e1008926 (2020).
  8. https://asia.ensembl.org/Ornithorhynchus_anatinus/Info/Annotation.
  9. Zhou, Y. et al. Platypus and echidna genomes reveal mammalian biology and evolution. Nature 592, 756–762 (2021).
  10. https://asia.ensembl.org/Gallus_gallus/Info/Annotation.
  11. https://www.ncbi.nlm.nih.gov/assembly/1489441.
  12. Holt, C. et al. Improved genome assembly and annotation for the rock pigeon (Columba livia). G3 Genes Genomes Genetics 8, g3.300443.2017 (2018).
  13. https://asia.ensembl.org/Dromaius_novaehollandiae/Info/Annotation.
  14. Sackton, T. B. et al. Convergent regulatory evolution and loss of flight in paleognathous birds. Science 364, 74–78 (2019).
  15. https://www.ncbi.nlm.nih.gov/assembly/GCA_000768395.2#/st.
  16. Ghosh, A. et al. A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae. Genome Biol Evol 12, 3635-3646 (2020).
  17. https://asia.ensembl.org/Pelodiscus_sinensis/Info/Annotation.
  18. Wang, Z. et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet 45, 701–706 (2013).
  19. https://asia.ensembl.org/Sphenodon_punctatus/Info/Annotation.
  20. Gemmell, N. J. et al. The tuatara genome reveals ancient features of amniote evolution. Nature 584, 403–409 (2020).
  21. https://www.ncbi.nlm.nih.gov/genome/381.
  22. Nowoshilow, S. et al. The axolotl genome and the evolution of key tissue formation regulators. Nature 554, 50–55 (2018).
  23. https://asia.ensembl.org/Xenopus_tropicalis/Info/Annotation.
  24. Karimi, K. et al. Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 46, D861–D868 (2018).
  25. https://www.ncbi.nlm.nih.gov/genome/7137?genome_assembly_id=1532268.
  26. Meyer, A. et al. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 590, 284–289 (2021).
  27. https://asia.ensembl.org/Latimeria_chalumnae/Info/Annotation.
  28. Amemiya, C. T. et al. The African coelacanth genome provides insights into tetrapod evolution. Nature 496, 311–316 (2013).
  29. https://asia.ensembl.org/Danio_rerio/Info/Annotation.
  30. https://asia.ensembl.org/Takifugu_rubripes/Info/Annotation.
  31. https://asia.ensembl.org/Hippocampus_comes/Info/Annotation.
  32. Lin, Q. et al. The seahorse genome and the evolution of its specialized morphology. Nature 540, 395–399 (2016).
  33. https://www.ncbi.nlm.nih.gov/genome/12366?genome_assembly_id=397945.
  34. Hara, Y. et al. Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nat Ecol Evol 2, 1761–1771 (2018).
  35. https://asia.ensembl.org/Eptatretus_burgeri/Info/Annotation
  36. Yamaguchi, K. et al. Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri. bioRxiv (2020). doi:10.1101/2020.07.24.218818
  37. https://asia.ensembl.org/Petromyzon_marinus/Info/Annotation
  38. Smith, J. J. et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 45, 415–421 (2013).
  39. https://stackoverflow.com/questions/55104819/display-count-on-top-of-seaborn-barplot

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