gganatogram

This function plots anatograms of specified tissues, species, and sex .

gganatogram(data = NULL, outline = TRUE, fillOutline = "lightgray",
  organism = "human", sex = "male", fill = "colour",
  anatogram = NULL, ggplot2_only = FALSE)

Arguments

data	The main data frame consisting of what organs to plot, colours, and values. Default is NULL
outline	logical indicating if the outline of the organism should be plotted
fillOutline	Fill colour of outline. Default is #a6bddb
organism	The organism to be plotted. Currently, only human is accepted.
sex	Sex of the organism
fill	How to fill
anatogram	A list, similar to hgMale_list that will create the outline and has the corresponding organ data.frames in that list
ggplot2_only	If TRUE, will try to use only ggplot2 functionality

Examples

library(ggplot2)
#First lets just plot the outline. Only male human is possible now
gganatogram(fillOutline='#a6bddb', organism='human',
sex='male', fill="colour")


gganatogram(fillOutline='#a6bddb', organism='human',
sex='female', fill="colour")


gganatogram(fillOutline='#a6bddb', organism='mouse',
sex='Male', fill="colour")



#To add organs, create a data frame with specified tissues


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=FALSE)


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



#We can also remove the outline
oplot = gganatogram(data=organPlot, outline=FALSE, fillOutline='#a6bddb',
organism='human', sex='male', fill="colour")
oplot


oplot + facet_wrap(~type)


library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
organPlot %>%
     dplyr::filter(type %in% 'circulation') %>%
 gganatogram(fillOutline='#a6bddb', organism='human',
 sex='male', fill="colour")


organPlot %>%
     dplyr::filter(type %in% c('circulation', 'nervous system')) %>%
 gganatogram(fillOutline='#a6bddb', organism='human',
 sex='male', fill="value") +
 theme_void() +
 scale_fill_gradient(low = "white", high = "red")



#Use hgMale_key to find all tissues to plot
hgMale_key = gganatogram::hgMale_key
head(hgMale_key)
#>               organ           type  colour     value
#> 1     thyroid_gland          other #41ab5d  4.672637
#> 2       bone_marrow          other #41ab5d  3.310015
#> 3    frontal_cortex nervous_system  purple 15.506890
#> 4 prefrontal_cortex nervous_system  purple  1.813205
#> 5   pituitary_gland          other #41ab5d 12.879309
#> 6             aorta    circulation     red 17.302852
all_tissues = gganatogram(data=hgMale_key, fillOutline='#a6bddb',
organism='human', sex='male', fill="colour")
all_tissues + theme_void()


all_tissues + theme_void() + facet_wrap(~type, ncol=3)



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

val_fill = gganatogram(data=hgMale_key, fillOutline='#a6bddb',
organism='human', sex='male', fill="value")
val_fill


col_fill +facet_wrap(~type, ncol=3) + theme_void()