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Prima Project

2018-09-11

MikuHatsune2018-09-11

gganatogram を使って人体を描く

こんなのを見かけた。

github

 

ggplot で人体を描いて、臓器やその臓器に与えられたパラメータに応じた色を描いてくれるらしい。

devtools::install_github("jespermaag/gganatogram")

library(ggplot2)
library(ggpolypath)
library(gganatogram)
library(dplyr)
library(gridExtra)

gganatogram(data=hgMale_key, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") + theme_void()

f:id:MikuHatsune:20180911125842p:image

 

hgMake_key にはデフォルトで入っている臓器とタイプ分け、タイプに応じた色が入っている。

                       organ           type    colour     value
1                bone marrow          other   #41ab5d  3.465121
2             frontal cortex nervous system    purple 16.279637
3          prefrontal cortex nervous system    purple 19.914552
4  gastroesophageal junction      digestion    orange  1.007031
5                     caecum      digestion    orange  1.805996
6                      ileum      digestion    orange  9.911434
7                     rectum      digestion    orange 19.989139
8                       nose          other   #41ab5d 12.858249
9                     tongue      digestion    orange  8.574843
10                     penis          other   #41ab5d 15.586977
11             nasal pharynx          other   #41ab5d 18.635302
12               spinal cord nervous system    purple 10.512042
13                    throat      digestion    orange 17.288282
14                 diaphragm    respiratory steelblue 10.941339
15                     liver      digestion    orange  5.335311
16                   stomach      digestion    orange  8.305132
17                    spleen      digestion    orange 16.728927
18                  duodenum      digestion    orange  4.879619
19              gall bladder      digestion    orange 14.012052
20                  pancreas      digestion    orange 10.786245
21                     colon      digestion    orange 16.293596
22           small intestine      digestion    orange  4.601459
23                  appendix          other   #41ab5d 12.857249
24           urinary bladder      digestion    orange  2.420635
25                      bone          other   #41ab5d  1.624326
26                 cartilage          other   #41ab5d 17.913499
27                 esophagus      digestion    orange 19.941666
28                      skin          other   #41ab5d  2.310034
29                     brain nervous system    purple 16.736891
30                     heart    circulation       red  8.383394
31                lymph_node    circulation       red 16.455134
32           skeletal_muscle          other   #41ab5d 19.707006
33                 leukocyte    circulation       red 10.528939
34             temporal_lobe nervous system    purple 16.984754
35          atrial_appendage          other   #41ab5d 17.094688
36           coronary_artery    circulation       red 13.996476
37               hippocampus nervous system    purple 15.832699
38              vas_deferens nervous system    purple 17.723010
39           seminal_vesicle          other   #41ab5d  1.047456
40                epididymis          other   #41ab5d 13.174310
41                    tonsil      digestion    orange  6.264270
42                      lung    respiratory steelblue 13.708475
43                   trachea      digestion    orange  1.825725
44                  bronchus    respiratory steelblue 14.416962
45                     nerve nervous system    purple 17.915368
46                    kidney      digestion    orange 15.225223

46臓器各々やろうと思ったけどfacet_grid がorgan をなぜか受け付けてくれないのでtype 別にプロットする。

gganatogram(data=hgMale_key, fillOutline=grey(0.9), organism='human', sex='male', fill="colour") +
  theme_void() +
  theme(title=element_text(size=24,face="bold")) +
  facet_grid(. ~ type)

ggsave("gganatogram.png", width=5, height=2)

f:id:MikuHatsune:20180911130022p:image

 

実際には、正常と病気で比較したいだろうから、例では癌として適当な図を作っている。

compareGroups <- rbind(data.frame(organ = c("heart", "leukocyte", "nerve", "brain", "liver", "stomach", "colon"), 
  colour = c("red", "red", "purple", "purple", "orange", "orange", "orange"), 
 value = c(10, 5, 1, 8, 2, 5, 5), 
 type = rep('Normal', 7), 
 stringsAsFactors=F),
 data.frame(organ = c("heart", "leukocyte", "nerve", "brain", "liver", "stomach", "colon"), 
  colour = c("red", "red", "purple", "purple", "orange", "orange", "orange"), 
 value = c(5, 5, 10, 8, 2, 5, 5), 
 type = rep('Cancer', 7), 
 stringsAsFactors=F))

gganatogram(data=compareGroups, fillOutline='#a6bddb', organism='human', sex='male', fill="value") + 
theme_void() +
facet_wrap(~type) +
scale_fill_gradient(low = "white", high = "red") 

f:id:MikuHatsune:20180911130152p:image

スパム対策のためのダミーです。もし見えても何も入力しないでください
ゲスト


画像認証

トラックバック - http://d.hatena.ne.jp/MikuHatsune/20180911/1536638589