Chapter 5 annoRect

This function can be used to add some rects annotations beside the plot or in plot.

Simple annotation:

library(jjAnno)
library(ggplot2)

# default plot
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1:10))

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

You can adjust the yPosition:

# adjust yPosition
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1:10),
         yPosition = c(11,11.5))

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

Change color alpha:

# change color alpha
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1:10),
         yPosition = c(11,11.5),
         alpha = 0.5)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

Set rect width:

# adjust rectWidth
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1:10),
         yPosition = c(11,11.5),
         rectWidth = 0.9)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

Change rect color and fill:

# change rect color and fill
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1:10),
         yPosition = c(11,11.5),
         rectWidth = 0.9,
         pCol = rep('black',10),
         pFill = rep('grey80',10))

## [1] "This palatte have 20 colors!"

Change rect lty and lwd:

# change rect lty and lwd
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1:10),
         yPosition = c(11,11.5),
         rectWidth = 0.9,
         pCol = rep('black',10),
         pFill = rep('grey80',10),
         lty = 'dashed',
         lwd = 2)

## [1] "This palatte have 20 colors!"

Add only partial annotations:

# only add some annotations
annoRect(object = p,
         annoPos = 'top',
         xPosition = c(1,3,5,7,9),
         yPosition = c(11,11.5))

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

Supply your own coordinates to annotate:

# supply your own coordinates to annotate
annoRect(object = p,
         annoPos = 'top',
         annoManual = T,
         xPosition = list(c(1,6),
                          c(5,10)),
         yPosition = c(11,11.5),
         pCol = rep('black',2),
         lty = 'solid',
         lwd = 2)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

You can supply multiple yPosition in list:

# multiple yPosition
annoRect(object = p,
         annoPos = 'top',
         annoManual = T,
         xPosition = list(c(1,6),
                          c(5,10)),
         yPosition = list(c(11,11.5),
                          c(11.5,12)),
         pCol = rep('black',2),
         lty = 'solid',
         lwd = 2)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

Add to right:

# add to right
annoRect(object = p,
         annoPos = 'right',
         yPosition = c(1:10),
         xPosition = c(10.5,11),
         rectWidth = 0.8)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

Add multiple annotations:

# add multiple
p1 <- annoRect(object = p,
               annoPos = 'top',
               xPosition = c(1:10),
               yPosition = c(11,11.5),
               rectWidth = 0.9,
               pCol = rep('black',10),
               pFill = rep('grey80',10),
               lty = 'dashed',
               lwd = 2)

## [1] "This palatte have 20 colors!"

# add second annotation
p2 <- annoRect(object = p1,
               annoPos = 'right',
               yPosition = c(1:10),
               xPosition = c(10.5,11),
               rectWidth = 0.8)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

# add third annotation
annoRect(object = p2,
         annoPos = 'top',
         xPosition = c(1:10),
         yPosition = c(11.8,12.3),
         rectWidth = 0.8)

## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"
## [1] "This palatte have 20 colors!"

5.1 add GO plot with annotation

Load test data:

data(pgo)

pgo

Here is the plot code:

# Plot
pgo <-
ggplot(df1,aes(x = log10PValue,y = Term)) +
  geom_point(aes(size = log10PValue,
                 color = log10PValue)) +
  scale_color_gradient2(low = 'blue',mid = 'green',high = 'red',
                        name = '',midpoint = 2.1) +
  scale_y_discrete(position = 'right') +
  scale_x_continuous(breaks = seq(0,2.8,0.4),limits = c(0,2.8)) +
  theme_grey(base_size = 14) +
  theme(legend.position = 'left',
        plot.margin = margin(t = 1,r = 1,b = 1,l = 1,unit = 'cm'),
        aspect.ratio = 2.5
        ) +
  coord_cartesian(clip = 'off') +
  ylab('')

5.2 annotate

Add 15 rects:

# another example annotation GO terms
annoRect(object = pgo,
         annoPos = 'right',
         yPosition = c(1:15),
         pCol = rep('transparent',15),
         pFill = rep(c('#F5F0BB','#C4DFAA','#90C8AC'),each = 5),
         xPosition = c(3,10),
         rectWidth = 1)

Supply own coordinates to add(3 rects):

# annotate mannually
annoRect(object = pgo,
         annoPos = 'right',
         annoManual = T,
         xPosition = c(3,10),
         yPosition = list(c(0.5,5.5,10.5),
                          c(5.5,10.5,15.5)),
         pCol = rep('black',3),
         pFill = c('#F5F0BB','#C4DFAA','#90C8AC'))