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library(oro.nifti) #for opening nii.gz files

## oro.nifti 0.11.4

## 
## Attaching package: 'oro.nifti'

## The following object is masked from 'package:dplyr':
## 
##     slice

library(RColorBrewer) #for color palettes
s_map1<-readNIfTI(system.file('seed_corr_1.nii.gz', package='ggBrain'))
s_map2<-readNIfTI(system.file('seed_corr_2.nii.gz', package='ggBrain'))
template <- readNIfTI(system.file('template.nii.gz', package='ggBrain'))
mask <- readNIfTI(system.file('brain_mask.nii.gz', package='ggBrain'))
seed_mask <- readNIfTI(system.file('seed_mask.nii.gz', package='ggBrain'))
nii1_trunc <- readNIfTI(system.file('subj_trunc_1.nii.gz', package='ggBrain'))
library(brainR)

## Loading required package: rgl

## Loading required package: misc3d

hd_template <- readNIfTI(system.file("MNI152_T1_1mm_brain.nii.gz", package="brainR"))
library(ggplot2)
#library(ggbrain)
library(devtools)

## Loading required package: usethis

#install_github('aaronjfisher/ggBrain')
library(ggBrain)
dd <- ggBrain(brains=hd_template,mask=hd_template>0,mar=3,
mar_ind=93,type='structural')


#dd
#now add aethetic changes with conventional ggplot code.
savep <- dd + scale_fill_continuous(low="black", high="white")+ theme_black_bg() 
ggsave(savep,filename = "slides\\02_neurodiversity\\img\\bw.png", dpi = 300)

## Saving 7 x 5 in image

## to access help pages

# Seed correlation map (stored in the array s_map1)
# mar=3 selects the Transverse plane, and mar_ind=30 selects the slice index.
#ddd<-ggBrain(brains=hd_template,mask=hd_template>0,
#            mar=3,
#    mar_ind=30,type='signed')

dd<-ggBrain(brains=list(s_map1@.Data-.2,s_map2@.Data+.1),
  brain_ind=c(1,1,1,2,2,2),
    template=template,
    mar=c(1,2,3,1,2,3),
    mar_ind=c(37,18,30,37,18,30),
    row_ind=c('ADHD','ADHD','ADHD','Normal','Normal','Normal'),
    col_ind=factor(c(1,2,3,1,2,3),labels=c('Sagittal','Coronal','Transverse')),
    mask=mask,type='signed',
    signed_colors = brewer.pal(9, 'RdYlGn')[c(1, 9)])
    
    #E:/Dropbox/Lab/Research/Presentations/slides/slides/02_neurodiversity/d00_slide.Rmd

 savep <- dd + ggtitle('Abnormal Activation (ADHD) vs Normal Brain Activation') +
  labs(subtitle="Red = Abnormal Activation, Green = Healthy Normal Brain Activation",
       caption="Extensive caption with irrelevant details to add visual clutter and cognitive overload. See supplemental material for additional unnecessary details.") +
  theme(
    plot.title = element_text(size = 10, color = "red", face="bold", family="Comic Sans MS"),
    plot.subtitle = element_text(size = 9, color =  "red", family="Comic Sans MS"),
    plot.caption = element_text(size = 6, color = "grey60", family="Comic Sans MS"),
    legend.title = element_text(size=6, family="Comic Sans MS"),
    legend.text = element_text(size=5, family="Comic Sans MS"),
    panel.background = element_rect(fill="black"),
    plot.background = element_rect(fill="grey20"),
    panel.grid.major = element_line(color="grey70", size=0.8),
    panel.grid.minor = element_line(color="grey50", linetype="dotted"))

## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

ggsave(savep,filename = "slides\\02_neurodiversity\\img\\lessnice.png", dpi = 300)

## Saving 7 x 5 in image

library(ggBrain)
library(RColorBrewer)

# Define neutral palette (e.g., viridis)
library(viridisLite)
neutral_colors <- viridis(9)

# Generate revised seed correlation maps
dd <- ggBrain(
  brains = list(s_map1@.Data - 0.2, s_map2@.Data + 0.1),
  brain_ind = c(1,1,1,2,2,2),
  template = template,
  mar = c(1,2,3,1,2,3),
  mar_ind = c(37,18,30,37,18,30),
  row_ind = c('Pattern A','Pattern A','Pattern A','Pattern B','Pattern B','Pattern B'),
  col_ind = factor(c(1,2,3,1,2,3), labels = c('Sagittal','Coronal','Transverse')),
  mask = mask,
  type = 'signed',
  signed_colors = neutral_colors[c(2, 7)] # Midpoints from neutral palette
) 

# Accessible theme and captions
savep <- dd + 
  ggtitle('Seed Correlation Maps Showing Two Neural Activation Patterns') + 
  labs(caption = "Patterns represent two commonly observed neurodevelopmental variations, illustrating differences without implying deficit or dysfunction.") +
  theme_minimal(base_size = 14)

# Save revised plot with neutral presentation
ggsave(savep, filename = "slides/02_neurodiversity/img/revised_seed_correlation.png", dpi = 300)

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ddd<-ggBrain(brains=list(s_map1@.Data-.2,s_map2@.Data+.1),
  brain_ind=c(1,1,1,2,2,2),
    template=template,
    mar=c(1,2,3,1,2,3),
    mar_ind=c(37,18,30,37,18,30),
    row_ind=c('ADHD','ADHD','ADHD','Typical','Typical','Typical'),
    col_ind=factor(c(1,2,3,1,2,3),labels=c('Sagittal','Coronal','Transverse')),
    mask=mask,
  type='signed',
    signed_colors = brewer.pal(9, 'PRGn')[c(1, 9)])

savep <- ddd + 
  ggtitle('Seed Correlation Maps Showing Two Neural Activation Patterns') + 
  labs(caption = "Patterns represent two commonly observed neurodevelopmental variations") +  theme_minimal(base_size = 14)
ggsave(savep,filename = "slides\\02_neurodiversity\\img\\morenice.png", dpi = 300)

## Saving 7 x 5 in image