gganatogram—基于 ggplot2 的解剖图和组织模块化可视化（动植物、细胞）
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组织动画热图介绍给大家。
安装 R 包
gganatogram：基于 ggplot2 的解剖图和组织模块化可视化的 R 包。
# install from Github
devtools::install_github("jespermaag/gganatogram")
devtools::install_github("mdsumner/ggpolypath")
案例演示
加载 R 包。
library(gganatogram)
library(ggpolypath)
library(dplyr)
library(viridis)
library(gridExtra)
人类男性
hgMale <- gganatogram(data=hgMale_key, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") + theme_void()
hgFemale <- gganatogram(data=hgFemale_key, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") + theme_void()
# mmMale <- gganatogram(data=mmMale_key, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour") + theme_void()
# mmFemale <- gganatogram(data=mmFemale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='female', fill="colour") +theme_void()
grid.arrange(hgMale, hgFemale, mmMale, mmFemale, ncol=4)
hgMale <- gganatogram(data=hgMale_key, fillOutline='#440154FF', organism='human', sex='male', fill="value") + theme_void() + scale_fill_viridis()
hgFemale <- gganatogram(data=hgFemale_key, fillOutline='#440154FF', organism='human', sex='female', fill="value") + theme_void() + scale_fill_viridis()
# mmMale <- gganatogram(data=mmMale_key, fillOutline='#440154FF', organism='mouse', sex='male', fill="value") + theme_void() + scale_fill_viridis()
# mmFemale <- gganatogram(data=mmFemale_key, outline = T, fillOutline='#440154FF', organism='mouse', sex='female', fill="value") +theme_void() + scale_fill_viridis()
grid.arrange(hgMale, hgFemale, mmMale, mmFemale, ncol=2)
数据格式大概是这样：
为了使用函数 gganatogram，如果需要，您需要有一个包含器官、颜色和值的数据框。
organPlot <- data.frame(organ = c("heart", "leukocyte", "nerve", "brain", "liver", "stomach", "colon"),
type = c("circulation", "circulation", "nervous system", "nervous system", "digestion", "digestion", "digestion"),
colour = c("red", "red", "purple", "purple", "orange", "orange", "orange"),
value = c(10, 5, 1, 8, 2, 5, 5),
stringsAsFactors=F)
head(organPlot)
#> organ type colour value
#> 1 heart circulation red 10
#> 2 leukocyte circulation red 5
#> 3 nerve nervous system purple 1
#> 4 brain nervous system purple 8
#> 5 liver digestion orange 2
#> 6 stomach digestion orange 5
使用函数 gganatogram 并使用颜色填充器官。
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="colour")
当然，我们可以使用ggplot主题和功能来调整图片。
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
theme_void()
我们还可以使用 hgMale_key绘制所有可用的组织。
hgMale_key$organ
#> [1] "thyroid_gland" "bone_marrow"
#> [3] "frontal_cortex" "prefrontal_cortex"
#> [5] "pituitary_gland" "aorta"
#> [7] "gastroesophageal_junction" "left_ventricle"
#> [9] "caecum" "ileum"
#> [11] "rectum" "nose"
#> [13] "breast" "tongue"
#> [15] "left_atrium" "pulmonary_valve"
#> [17] "mitral_valve" "penis"
#> [19] "nasal_pharynx" "spinal_cord"
#> [21] "throat" "tricuspid_valve"
#> [23] "diaphragm" "liver"
#> [25] "stomach" "spleen"
#> [27] "duodenum" "gall_bladder"
#> [29] "pancreas" "colon"
#> [31] "small_intestine" "appendix"
#> [33] "smooth_muscle" "urinary_bladder"
#> [35] "bone" "cartilage"
#> [37] "esophagus" "salivary_gland"
#> [39] "parotid_gland" "submandibular_gland"
#> [41] "skin" "pleura"
#> [43] "brain" "heart"
#> [45] "adrenal_gland" "lymph_node"
#> [47] "adipose_tissue" "skeletal_muscle"
#> [49] "leukocyte" "temporal_lobe"
#> [51] "atrial_appendage" "coronary_artery"
#> [53] "hippocampus" "vas_deferens"
#> [55] "seminal_vesicle" "epididymis"
#> [57] "tonsil" "lung"
#> [59] "amygdala" "trachea"
#> [61] "bronchus" "nerve"
#> [63] "cerebellum" "cerebellar_hemisphere"
#> [65] "kidney" "renal_cortex"
#> [67] "testis" "prostate"
gganatogram(data=hgMale_key, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +theme_void()
我们也可以跳过绘制图形的轮廓。
organPlot %>%
dplyr::filter(type %in% c('circulation', 'nervous system')) %>%
gganatogram(outline=F, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
theme_void()
我们可以根据给每个器官的值来填充组织。
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="value") +
theme_void() +
scale_fill_gradient(low = "white", high = "red")
我们还可以使用 facet_wrap 来比较组。
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")
您还可以在保留轮廓的同时将组织分成不同类型。
gganatogram(data=hgMale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
facet_wrap(~type, ncol=4) +
theme_void()
人类女性
hgFemale_key$organ
#> [1] "atrial_appendage" "ectocervix"
#> [3] "hippocampus" "pleura"
#> [5] "bronchus" "trachea"
#> [7] "lung" "tonsil"
#> [9] "submandibular_gland" "breast"
#> [11] "spinal_cord" "pancreas"
#> [13] "liver" "colon"
#> [15] "bone_marrow" "urinary_bladder"
#> [17] "stomach" "duodenum"
#> [19] "esophagus" "gall_bladder"
#> [21] "spleen" "small_intestine"
#> [23] "placenta" "endometrium"
#> [25] "vagina" "aorta"
#> [27] "pituitary_gland" "gastroesophageal_junction"
#> [29] "caecum" "appendix"
#> [31] "ileum" "left_atrium"
#> [33] "left_ventricle" "pulmonary_valve"
#> [35] "mitral_valve" "diaphragm"
#> [37] "bone" "cartilage"
#> [39] "throat" "rectum"
#> [41] "nasal_septum" "nasal_pharynx"
#> [43] "cerebellum" "cerebellar_hemisphere"
#> [45] "prefrontal_cortex" "frontal_cortex"
#> [47] "nose" "temporal_lobe"
#> [49] "cerebral_cortex" "kidney"
#> [51] "renal_cortex" "coronary_artery"
#> [53] "tricuspid_valve" "thyroid_gland"
#> [55] "skin" "parotid_gland"
#> [57] "adipose_tissue" "heart"
#> [59] "smooth_muscle" "brain"
#> [61] "adrenal_gland" "lymph_node"
#> [63] "skeletal_muscle" "ovary"
#> [65] "leukocyte" "salivary_gland"
#> [67] "fallopian_tube" "uterus"
#> [69] "uterine_cervix" "nerve"
gganatogram(data=hgFemale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") +theme_void()
轮廓显示女性生殖系统：
hgFemale_key %>%
dplyr::filter(type=='reproductive') %>%
gganatogram( outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") +
theme_void() +
coord_cartesian(xlim = c(30, 75), ylim = c(-110, -80))
雄鼠组织
mmMale_key$organ
#> [1] "aorta" "brown_adipose_tissue"
#> [3] "stomach" "duodenum"
#> [5] "pancreas" "spleen"
#> [7] "adrenal_gland" "kidney"
#> [9] "colon" "small_intestine"
#> [11] "caecum" "jejunum"
#> [13] "ileum" "esophagus"
#> [15] "gall_bladder" "lymph_node"
#> [17] "seminal_vesicle" "penis"
#> [19] "femur" "bone_marrow"
#> [21] "cartilage" "quadriceps_femoris"
#> [23] "spinal_cord" "lung"
#> [25] "diaphragm" "trachea"
#> [27] "hindlimb" "trigeminal_nerve"
#> [29] "sciatic_nerve" "intestinal_mucosa"
#> [31] "liver" "heart"
#> [33] "brain" "skeletal_muscle"
#> [35] "circulatory_system" "blood_vessel"
#> [37] "skin" "prostate_gland"
#> [39] "vas_deferens" "epididymis"
#> [41] "testis" "urinary_bladder"
#> [43] "thymus" "peripheral_nervous_system"
#> [45] "eye"
gganatogram(data=mmMale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour") +theme_void() +coord_fixed()
雌鼠组织
mmFemale_key$organ
#> [1] "aorta" "circulatory_system"
#> [3] "brown_adipose_tissue" "stomach"
#> [5] "duodenum" "pancreas"
#> [7] "spleen" "adrenal_gland"
#> [9] "kidney" "colon"
#> [11] "small_intestine" "caecum"
#> [13] "jejunum" "ileum"
#> [15] "esophagus" "gall_bladder"
#> [17] "vagina" "uterus"
#> [19] "urinary_bladder" "tongue"
#> [21] "Peyer's_patch" "femur"
#> [23] "bone_marrow" "cartilage"
#> [25] "quadriceps_femoris" "skeletal_muscle"
#> [27] "spinal_cord" "diaphragm"
#> [29] "hindlimb" "trigeminal_nerve"
#> [31] "eye" "intestinal_mucosa"
#> [33] "brain" "heart"
#> [35] "liver" "sciatic_nerve"
#> [37] "blood_vessel" "skin"
#> [39] "mammary_gland" "title8178"
#> [41] "reproductive_system" "lymph_node"
#> [43] "thymus" "thyroid_gland"
#> [45] "lung" "peripheral_nervous_system"
#> [47] "trachea"
gganatogram(data=mmFemale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='female', fill="colour") +theme_void() +coord_fixed()
细胞结构
可以使用 cell_key 访问细胞数据。
length(cell_key)
#> [1] 1
cell_key
#> $cell
#> organ type colour value
#> 1 cytosol other steelblue 2.07159434
#> 4 intermediate_filaments other #984EA3 14.89497057
#> 6 actin_filaments other #FFFF33 5.87440944
#> 8 focal_adhesion_sites other #F781BF 8.12483660
#> 10 microtubule_organizing_center other #66C2A5 8.67564889
#> 12 centrosome other #8DA0CB 1.02852838
#> 13 microtubules other #E78AC3 9.48882657
#> 16 microtubule_ends other #E5C494 4.80457195
#> 18 secreted_proteins other #8DD3C7 9.20191105
#> 20 lipid_droplets other #BEBADA 3.48903574
#> 22 lysosomes other #80B1D3 3.73790434
#> 24 peroxisomes other #B3DE69 6.79465458
#> 26 endosomes other #D9D9D9 13.48636296
#> 28 endoplasmic_reticulum other #CCEBC5 11.36654344
#> 30 golgi_apparatus other #7FC97F 11.29225961
#> 32 nucleoplasm other #FDC086 2.07964782
#> 34 nuclear_membrane other #386CB0 7.98595837
#> 36 nuclear_bodies other #BF5B17 0.05868359
#> 38 nuclear_speckles other #1B9E77 0.61672243
#> 40 nucleoli other #7570B3 14.96900579
#> 42 nucleoli_fibrillar_center other #66A61E 8.72324527
#> 44 rods_and_rings other #A6761D 9.53194209
#> 46 mitochondria other #A6CEE3 1.29396698
#> 48 plasma_membrane other #B2DF8A 13.45657571
要使用颜色或值绘制整个细胞，请使用以下命令。如果要指定背景颜色，则必须移除胞质溶胶或将胞质溶胶的颜色更改为所需的颜色。
gganatogram(data=cell_key[['cell']], outline = T, fillOutline='steelblue', organism="cell", fill="colour") +theme_void() + coord_fixed()
gganatogram(data=cell_key[['cell']], outline = T, fillOutline='lightgray', organism="cell", fill="value") +theme_void() + coord_fixed() + scale_fill_viridis()
其他物种
length(other_key)
#> [1] 24
names(other_key)
#> [1] "anolis_carolinensis"
#> [2] "arabidopsis_thaliana"
#> [3] "bos_taurus"
#> [4] "brachypodium_distachyon.flower_parts"
#> [5] "brachypodium_distachyon.whole_plant"
#> [6] "gallus_gallus"
#> [7] "hordeum_vulgare.flower_parts"
#> [8] "hordeum_vulgare.whole_plant"
#> [9] "macaca_mulatta"
#> [10] "monodelphis_domestica"
#> [11] "oryza_sativa.flower_parts"
#> [12] "oryza_sativa.whole_plant"
#> [13] "papio_anubis"
#> [14] "rattus_norvegicus"
#> [15] "solanum_lycopersicum.flower_parts"
#> [16] "solanum_lycopersicum.whole_plant"
#> [17] "sorghum_bicolor.flower_parts"
#> [18] "sorghum_bicolor.whole_plant"
#> [19] "tetraodon_nigroviridis"
#> [20] "triticum_aestivum.flower_parts"
#> [21] "triticum_aestivum.whole_plant"
#> [22] "xenopus_tropicalis"
#> [23] "zea_mays.flower_parts"
#> [24] "zea_mays.whole_plant"
画个牛。
other_key[["bos_taurus"]]
#> organ type colour value
#> 2 duodenum other #E41A1C 11.381132
#> 3 brain other #377EB8 2.264810
#> 4 kidney other #4DAF4A 4.131599
#> 5 lung other #984EA3 3.182946
#> 6 colon other #FF7F00 3.114481
#> 7 heart other #FFFF33 13.141334
#> 8 liver other #A65628 17.251310
#> 9 pulmonary vein other #F781BF 13.414659
#> 19 UBERON_0001013 other #999999 12.126515
#> 20 UBERON_0001013 other #66C2A5 1.898023
#> 21 UBERON_0001013 other #FC8D62 19.290389
#> 22 UBERON_0014892 other #8DA0CB 10.994221
#> 23 UBERON_0014892 other #E78AC3 16.761115
#> 24 UBERON_0014892 other #A6D854 2.468627
#> 25 UBERON_0014892 other #FFD92F 1.556285
#> 26 UBERON_0014892 other #E5C494 3.461740
#> 27 UBERON_0014892 other #B3B3B3 18.595027
gganatogram(data=other_key[["bos_taurus"]], outline = T, fillOutline='white', organism="bos_taurus", sex='female', fill="colour") +
theme_void() +
ggtitle("bos_taurus") +
theme(plot.title = element_text(hjust=0.5)) +
coord_fixed()
这是一种遍历所有其他生物并绘制其器官的方法。
library(gridExtra)
plotList <- list()
for (organism in names(other_key)) {
plotList[[organism]] <- gganatogram(data=other_key[[organism]], outline = T, fillOutline='white', organism=organism, sex='female', fill="colour") +
theme_void() +
ggtitle(organism) +
theme(plot.title = element_text(hjust=0.5, size=9)) +
coord_fixed()
}
do.call(grid.arrange, c(plotList[1:4], ncol=2))
do.call(grid.arrange, c(plotList[5:8], ncol=2))
do.call(grid.arrange, c(plotList[9:12], ncol=2))
do.call(grid.arrange, c(plotList[13:16], ncol=2))
do.call(grid.arrange, c(plotList[17:20], ncol=2))
do.call(grid.arrange, c(plotList[21:24], ncol=2))
参考链接
https://www.ebi.ac.uk/gxa/home https://github.com/jespermaag/gganatogram https://github.com/ebi-gene-expression-group/anatomogram
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