gganatogram
Create anatogram images for different organisms. For now only human male is available. This package uses the tissue coordinates from the figure in Expression Atlas. https://www.ebi.ac.uk/gxa/home https://github.com/ebi-gene-expression-group/anatomogram
If you use gganatogram please cite Expression Atlas as well. Petryszak et al. 2015 Petryszak, Robert, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe et al. "Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants." Nucleic acids research 44, no. D1 (2015): D746-D752.
More plot examples can be found at https://jespermaag.github.io/blog/2018/gganatogram/
Install
Install from github using devtools.
## install from Github
devtools::install_github("jespermaag/gganatogram")Usage
This package requires ggplot2 and ggpolypath which loads when loading the package
library(gganatogram)
library(dplyr)Available organisms
library(gridExtra)
#> Warning: package 'gridExtra' was built under R version 3.4.1
#>
#> Attaching package: 'gridExtra'
#> The following object is masked from 'package:dplyr':
#>
#> combine
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)In order to use the function gganatogram, you need to have a data frame with organ, colour, and value if you want to.
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 5Using the function gganatogram with the filling the organs based on colour.
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="colour")Of course, we can use the ggplot themes and functions to adjust the plots
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
theme_void()We can also plot all tissues available using hgMale_key
hgMale_key$organ
#> [1] "bone_marrow" "frontal_cortex"
#> [3] "prefrontal_cortex" "aorta"
#> [5] "gastroesophageal_junction" "left_ventricle"
#> [7] "caecum" "ileum"
#> [9] "rectum" "nose"
#> [11] "tongue" "left_atrium"
#> [13] "pulmonary_valve" "mitral_valve"
#> [15] "penis" "nasal_pharynx"
#> [17] "spinal_cord" "throat"
#> [19] "tricuspid_valve" "diaphragm"
#> [21] "liver" "stomach"
#> [23] "spleen" "duodenum"
#> [25] "gall_bladder" "pancreas"
#> [27] "colon" "small_intestine"
#> [29] "appendix" "smooth_muscle"
#> [31] "urinary_bladder" "bone"
#> [33] "cartilage" "esophagus"
#> [35] "skin" "pleura"
#> [37] "brain" "heart"
#> [39] "lymph_node" "adipose_tissue"
#> [41] "skeletal_muscle" "leukocyte"
#> [43] "temporal_lobe" "atrial_appendage"
#> [45] "coronary_artery" "hippocampus"
#> [47] "vas_deferens" "seminal_vesicle"
#> [49] "epididymis" "tonsil"
#> [51] "lung" "trachea"
#> [53] "bronchus" "nerve"
#> [55] "cerebellum" "cerebellar_hemisphere"
#> [57] "kidney" "renal_cortex"
gganatogram(data=hgMale_key, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +theme_void()We can also skip plotting the outline of the graph
organPlot %>%
dplyr::filter(type %in% c('circulation', 'nervous system')) %>%
gganatogram(outline=F, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
theme_void()
#> Warning: package 'bindrcpp' was built under R version 3.4.4We can fill the tissues based on the values given to each organ
gganatogram(data=organPlot, fillOutline='#a6bddb', organism='human', sex='male', fill="value") +
theme_void() +
scale_fill_gradient(low = "white", high = "red")We can also use facet_wrap to compare groups. First create add two data frames together with different values and the conditions in the type column
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") You can also split the tissues into types while retaining the outline
gganatogram(data=hgMale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='male', fill="colour") +
facet_wrap(~type, ncol=4) +
theme_void()Added female option
All female tissues
hgFemale_key$organ
#> [1] "pancreas" "liver"
#> [3] "colon" "bone_marrow"
#> [5] "urinary_bladder" "stomach"
#> [7] "duodenum" "esophagus"
#> [9] "gall_bladder" "spleen"
#> [11] "small_intestine" "placenta"
#> [13] "endometrium" "vagina"
#> [15] "aorta" "gastroesophageal_junction"
#> [17] "caecum" "appendix"
#> [19] "ileum" "left_atrium"
#> [21] "left_ventricle" "pulmonary_valve"
#> [23] "mitral_valve" "diaphragm"
#> [25] "bone" "cartilage"
#> [27] "throat" "rectum"
#> [29] "nasal_septum" "nasal_pharynx"
#> [31] "cerebellum" "cerebellar_hemisphere"
#> [33] "prefrontal_cortex" "frontal_cortex"
#> [35] "nose" "temporal_lobe"
#> [37] "cerebral_cortex" "kidney"
#> [39] "renal_cortex" "coronary_artery"
#> [41] "tricuspid_valve" "skin"
#> [43] "adipose_tissue" "heart"
#> [45] "smooth_muscle" "brain"
#> [47] "lymph_node" "skeletal_muscle"
#> [49] "ovary" "leukocyte"
#> [51] "fallopian_tube" "uterus"
#> [53] "uterine_cervix" "nerve"
#> [55] "atrial_appendage" "ectocervix"
#> [57] "hippocampus" "pleura"
#> [59] "bronchus" "trachea"
#> [61] "lung" "tonsil"
#> [63] "spinal_cord"
gganatogram(data=hgFemale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") +theme_void()You can also split the tissues into types while retaining the outline
gganatogram(data=hgFemale_key, outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") +
facet_wrap(~type, ncol=4) +
theme_void()To display the female reproductive system with outline.
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))Added mouse
Male
mmMale_key$organ
#> [1] "aorta" "brown_adipose_tissue"
#> [3] "stomach" "duodenum"
#> [5] "pancreas" "spleen"
#> [7] "adrenal_gland" "kidney"
#> [9] "colon" "small_intestine"
#> [11] "caecum" "jejunum"
#> [13] "ileum" "esophagus"
#> [15] "gall_bladder" "lymph_node"
#> [17] "seminal_vesicle" "penis"
#> [19] "femur" "bone_marrow"
#> [21] "cartilage" "quadriceps_femoris"
#> [23] "spinal_cord" "lung"
#> [25] "diaphragm" "trachea"
#> [27] "hindlimb" "trigeminal_nerve"
#> [29] "sciatic_nerve" "intestinal_mucosa"
#> [31] "liver" "heart"
#> [33] "brain" "skeletal_muscle"
#> [35] "circulatory_system" "blood_vessel"
#> [37] "skin" "prostate_gland"
#> [39] "vas_deferens" "epididymis"
#> [41] "testis" "urinary_bladder"
#> [43] "thymus" "peripheral_nervous_system"
#> [45] "eye"
gganatogram(data=mmMale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour") +theme_void()
gganatogram(data=mmMale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='male', fill="colour") +theme_void()+facet_wrap(~type, ncol=4)Feale
mmFemale_key$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()
gganatogram(data=mmFemale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='female', fill="colour") +theme_void()+facet_wrap(~type, ncol=4)