Gradient fill in ggplot2 - r

Say if have the following plot.
library(ggplot2)
n <- 1169
df22 <- data.frame(x = 1:n, val = seq(0, 0.5, length.out = n), type = 1)
ggplot(df22, aes(x = x, y = val)) +
geom_ribbon(aes(ymax = val, ymin = 0, fill = type, group = type))
Instead of the blue color i would like to have a Gradient fill (from blue to red - vertically. So starting with blue at the bottom and red on top with a Parameter to Control the smoothness of Color change).
I found the following resource:
https://ggplot2.tidyverse.org/reference/scale_gradient.html
Unfortunately, it didnt work out for me as my data is not continous(?).

The following code will do it (but horizontally):
library(scales) # for muted
ggplot(df22, aes(x = x, y = val)) +
geom_ribbon(aes(ymax = val, ymin = 0, group = type)) +
geom_col(aes(fill = val)) +
scale_fill_gradient2(position="bottom" , low = "blue", mid = muted("blue"), high = "red",
midpoint = median(df22$val))
If you want to make it vertically, you may flip the coordinates using coord_flip() upside down.
ggplot(df22, aes(x = val, y = x)) +
geom_ribbon(aes(ymax = val, ymin = 0)) +
coord_flip() +
geom_col(aes(fill = val)) +
scale_fill_gradient2(position="bottom" , low = "blue", mid = muted("blue"), high = "red",
midpoint = median(df22$val))
Or, if you want it to be horizontal with a vertical gradient (as you requested), you might need to go around it by playing with your data and using the geom_segment() instead of geom_ribbon(), like the following:
vals <- lapply(df22$val, function(y) seq(0, y, by = 0.001))
y <- unlist(vals)
mid <- rep(df22$x, lengths(vals))
d2 <- data.frame(x = mid - 1, xend = mid + 1, y = y, yend = y)
ggplot(data = d2, aes(x = x, xend = xend, y = y, yend = yend, color = y)) +
geom_segment(size = 1) +
scale_color_gradient2(low = "blue", mid = muted("blue"), high = "red", midpoint = median(d2$y))
This will give you the following:
Hope you find it helpful.

Related

ggplot geom_rect color gradient (without reference to data)?

I was wondering if it is possible to have a geom_rect with a color gradient without a data reference, i.e. outside of aes().
I would like the two rectangles in the bottom of the following plot to show a color gradient from red to white (left to right) and the top one to show a color gradient from yellow to white.
Is this possible in a simple way or do I have to create data to refer to?
ggplot() +
geom_rect(aes(xmin = c(1, 3), xmax = c(2.5, 4), ymin = c(1, 1), ymax = c(2, 2)), color = "black", fill = "red") +
geom_rect(aes(xmin = 1, xmax = 3.5, ymin = 3, ymax = 4), color = "black", fill = "yellow") +
theme_bw() +
theme(panel.grid = element_blank())
I tried to use scale_fill_gradient with geom_tile but this doesn't really do what I want: 1. the two supposed-to-be-red rectangles share a gradient and don't start with pure red each and 2. I can't manage to use two different scale_fill_gradient's in one plot.
foo <- tibble(x = seq(from = 1, to = 2.5, by = 0.001),
y = rep(1, 1501))
bar <- tibble(x = seq(from = 3, to = 4, by = 0.001),
y = rep(1, 1001))
foobar <- tibble(x = seq(from = 1, to = 3.5, by = 0.001),
y = rep(3, 2501))
ggplot() +
geom_tile(data = foo, aes(x = x, y = y, fill = x)) +
geom_tile(data = bar, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'red', high = 'white') +
geom_tile(data = foobar, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'yellow', high = 'white') +
theme_bw() +
theme(panel.grid = element_blank())
You could use the function new_scale_fill from ggnewscale between your two different scale_fill_gradient functions in your plot process. This will reset your aesthetics to make it possible to use another gradient like this:
library(tibble)
foo <- tibble(x = seq(from = 1, to = 2.5, by = 0.001),
y = rep(1, 1501))
bar <- tibble(x = seq(from = 3, to = 4, by = 0.001),
y = rep(1, 1001))
foobar <- tibble(x = seq(from = 1, to = 3.5, by = 0.001),
y = rep(3, 2501))
library(ggplot2)
library(ggnewscale)
ggplot() +
geom_tile(data = foo, aes(x = x, y = y, fill = x)) +
geom_tile(data = bar, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'red', high = 'white') +
new_scale_fill() +
geom_tile(data = foobar, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'yellow', high = 'white') +
theme_bw() +
theme(panel.grid = element_blank())
Created on 2022-09-23 with reprex v2.0.2
To add for each geom_tile a gradient color, you could use for each tile new_scale_fill like this:
library(ggplot2)
library(ggnewscale)
ggplot() +
geom_tile(data = foo, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'red', high = 'white', guide = 'none') +
new_scale_fill() +
geom_tile(data = bar, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'red', high = 'white') +
new_scale_fill() +
geom_tile(data = foobar, aes(x = x, y = y, fill = x)) +
scale_fill_gradient(low = 'yellow', high = 'white') +
theme_bw() +
theme(panel.grid = element_blank())
Created on 2022-09-23 with reprex v2.0.2

How to use geom_ribbon()?

Here is my example.
library(ggplot2)
my_df <- data.frame(x = c(1,2,3), y = c(4,5,6), y_min = c(1,1,2),
y_max = c(7,8,8))
ggplot(data = my_df)+
geom_line(aes(x = x, y = y, color = "blue"))+
geom_ribbon(aes(ymin =y_min, ymax =y_max, x= x), fill = "grey70")
I would like to get back something resembling line plot and confidence interval around it, but I am only getting confidence interval (ribbon) not the main line.
What am I missing?
We could set alpha = 0.3 to see the line and change grey70 to grey grey12:
ggplot(my_df) + geom_line(aes(y=y, x=x, colour = "blue"))+
geom_ribbon(aes(ymin=y_min, ymax=y_max, x=x, fill = "band"), alpha = 0.3)+
scale_colour_manual("",values="blue")+
scale_fill_manual("",values="grey12")

Use a gradient color fill for a bubble grid chart

I've got a bubble grid chart created but I can't for the life of my change the colors of the fill. I want to use a rainbow gradient based on the values. Below is my code and I've attached image out my output
setwd("C:/Users/Schelly/Desktop/Projects/Jens_tables_and_figures_2020/Bubble_chart")
library(tidyverse)
library(reshape2)
pc <- read.csv("Para_Bubble_data2.csv", header = TRUE)
head(pc)
pcm<-melt(pc, id = c("Sample"))
pcm$Sample <- factor(pcm$Sample,levels=unique(pcm$Sample))
xx = ggplot(pcm, aes(x = Sample, y = variable)) +
geom_point(aes(size = value, fill = value), alpha = 0.75, shape = 21) +
scale_colour_gradientn(colours=rainbow(4))+
scale_size_continuous(limits = c(0.000001, 1), range = c(1,17), breaks = c(.01,.10,.50,.75)) +
labs( x= "", y = "", size = "Relative Abundance (%)", fill = "")
xx
Output of code
You need to specify aes(colour = value) if you want to use scale_color_gradientn:
library(ggplot2)
df <- data.frame(x = factor(rep(1:5, each = 6)),
y = factor(rep(1:6, 5)), val = sample(30))
ggplot(df, aes(x = x, y = y, size = val, colour = val)) +
geom_point() +
scale_color_gradientn(colours = c("red", "yellow", "blue"))
If you want to use fill (to preserve a different outline colour), you need to use scale_fill_gradientn:
ggplot(df, aes(x = x, y = y, size = val)) +
geom_point(aes(size = val, fill = val), alpha = 0.75, shape = 21) +
scale_fill_gradientn(colours = rainbow(4))+
labs( x= "", y = "", size = "Relative Abundance (%)", fill = "")

geom_rect equivalent of vjust and hjust [duplicate]

I use an example from here. My question is how can I add a specific bounding box to this heatmap, such as add a red line box to the top left four tiles?
require(ggplot2)
require(reshape)
require(scales)
mydf <- data.frame(industry = c('all industries','steel','cars'),
'all regions' = c(250,150,100), americas = c(150,90,60),
europe = c(150,60,40), check.names = FALSE)
mydf
mymelt <- melt(mydf, id.var = c('industry'))
mymelt
ggplot(mymelt, aes(x = industry, y = variable, fill = value)) +
geom_tile() + geom_text(aes(fill = mymelt$value, label = mymelt$value))
A quick and dirty (some hard-coding) possibility is to use geom_rect, where the positions are given by the numerical values of the levels of x and y variables to be bound with a box, plus/minus an offset.
ggplot(mymelt, aes(x = industry, y = variable, fill = value, label = value)) +
geom_tile() +
geom_text() +
geom_rect(aes(xmin = 1 - 0.5, xmax = 2 + 0.5, ymin = 2 - 0.5, ymax = 3 + 0.5),
fill = "transparent", color = "red", size = 1.5)
A less hard-coded version:
# convert x and y variables to factors
ind <- as.factor(mymelt$industry)
vars <- as.factor(mymelt$variable)
# numeric version of the levels to be bound by a box
xmin <- unique(as.numeric(ind[ind == "all industries"]))
xmax <- unique(as.numeric(ind[ind == "cars"]))
ymin <- unique(as.numeric(vars[vars == "americas"]))
ymax <- unique(as.numeric(vars[vars == "europe"]))
# set offset
offset <- 0.5
ggplot(mymelt, aes(x = industry, y = variable, fill = value, label = value)) +
geom_tile() +
geom_text() +
geom_rect(aes(xmin = xmin - offset,
xmax = xmax + offset,
ymin = ymin - offset,
ymax = ymax + offset),
fill = "transparent", color = "red", size = 1.5)

How to add bounding box to a specific area in ggplot2 heatmap?

I use an example from here. My question is how can I add a specific bounding box to this heatmap, such as add a red line box to the top left four tiles?
require(ggplot2)
require(reshape)
require(scales)
mydf <- data.frame(industry = c('all industries','steel','cars'),
'all regions' = c(250,150,100), americas = c(150,90,60),
europe = c(150,60,40), check.names = FALSE)
mydf
mymelt <- melt(mydf, id.var = c('industry'))
mymelt
ggplot(mymelt, aes(x = industry, y = variable, fill = value)) +
geom_tile() + geom_text(aes(fill = mymelt$value, label = mymelt$value))
A quick and dirty (some hard-coding) possibility is to use geom_rect, where the positions are given by the numerical values of the levels of x and y variables to be bound with a box, plus/minus an offset.
ggplot(mymelt, aes(x = industry, y = variable, fill = value, label = value)) +
geom_tile() +
geom_text() +
geom_rect(aes(xmin = 1 - 0.5, xmax = 2 + 0.5, ymin = 2 - 0.5, ymax = 3 + 0.5),
fill = "transparent", color = "red", size = 1.5)
A less hard-coded version:
# convert x and y variables to factors
ind <- as.factor(mymelt$industry)
vars <- as.factor(mymelt$variable)
# numeric version of the levels to be bound by a box
xmin <- unique(as.numeric(ind[ind == "all industries"]))
xmax <- unique(as.numeric(ind[ind == "cars"]))
ymin <- unique(as.numeric(vars[vars == "americas"]))
ymax <- unique(as.numeric(vars[vars == "europe"]))
# set offset
offset <- 0.5
ggplot(mymelt, aes(x = industry, y = variable, fill = value, label = value)) +
geom_tile() +
geom_text() +
geom_rect(aes(xmin = xmin - offset,
xmax = xmax + offset,
ymin = ymin - offset,
ymax = ymax + offset),
fill = "transparent", color = "red", size = 1.5)

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