gganatogram: gganatogram

In neuroconductor-devel-releases/gganatogram: Create Anatograms of Various Species

Description

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

Usage

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)
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)
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()

neuroconductor-devel-releases/gganatogram documentation built on May 21, 2020, 1:03 p.m.