I have dataframe which represents sales by model within 2 different years. 'change' column stands for absolute change by models from 2020 to 2021 while 'chng.percent' measures this change in percentages.
However, I am struggling to apply the given Code of slope plot to my data.
df <- data.frame (model = c("A", "A", "B","B"),
year = c(2020,2021,2020,2021),
sale =c(105,190,110,180),
chang = c(85,NA,70,NA),
chng.percent = c(80.9,NA, 63.6,NA))
Expected outcome (Like this)
Here's a way to do it all within ggplot using your existing data:
ggplot(df, aes(year, sale, color = model)) +
geom_line(arrow = arrow(type = "closed", angle = 20),
key_glyph = draw_key_point) +
geom_vline(aes(xintercept = year)) +
geom_text(aes(label = sale, hjust = ifelse(year == 2020, 1.3, -0.3)),
color = "black",
size = 6) +
geom_text(aes(x = min(df$year) + 0.25, y = 105,
label = paste0("+", chang[1], "; ", chng.percent[1], "%"),
color = "A"), size = 5) +
geom_text(aes(x = max(df$year) - 0.25, y = 150,
label = paste0("+", chang[3], "; ", chng.percent[3], "%"),
color = "B"), size = 5) +
theme_void(base_size = 16) +
coord_cartesian(clip = "off") +
scale_x_continuous(breaks = c(2020, 2021)) +
guides(color = guide_legend(override.aes = list(size = 5))) +
scale_color_brewer(palette = "Set1") +
theme(plot.margin = margin(30, 30, 30, 30),
aspect.ratio = 1.5,
axis.text.x = element_text(size = 20))
you can try something like this :
df <- data.frame(model = c("A", "B"),
sale_2020 =c(105,110),
sale_2021 =c(190,180),
chang = c(85,70),
chng.percent = c(80.9, 63.6))
df %>%
ggplot() +
geom_segment(aes(x = 1, xend = 2,
y = sale_2020,
yend = sale_2021,
group = model,
col = model),
size = 1.2) +
# set the colors
scale_color_manual(values = c("#468189", "#9DBEBB"), guide = "none") +
# remove all axis stuff
theme_classic() +
theme(axis.line = element_blank(),
axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank()) +
geom_text(aes(x = x, y = y, label = label),
data = data.frame(x = 1:2,
y = 10 + max(df$sale_2021),
label = c("2020", "2021")),
col = "grey30",
size = 6) +
# add vertical lines that act as axis for 2020
geom_segment(x = 1, xend = 1,
y = min(df$sale_2020) -10,
yend = max(df$sale_2020) + 81,
col = "grey70", size = 1.5) +
# add vertical lines that act as axis for 2021
geom_segment(x = 2, xend = 2,
y = min(df$sale_2021) - 80,
yend = max(df$sale_2021) + 1,
col = "grey70", size = 1.5) +
# add the success rate next to each point on 2021 axis
geom_text(aes(x = 2 + 0.08,
y = sale_2021,
label = paste0(round(sale_2021, 1))),
col = "grey30") +
# add the success rate next to each point on 2021 axis
geom_text(aes(x = 1 - 0.08,
y = sale_2020,
label = paste0(round(sale_2020, 1))),
col = "grey30") +
# add the success rate next to each point on 2020 axis
geom_text(aes(x = 2 - 0.5,
y = c(156, 135),
label = paste0(round(chng.percent, 1), "%")),
col = "grey30")
Related
I have this data frame :
Raw.Score = c(0,1,2,3,4,5,6,7,8)
Severity = c(-3.56553994,-2.70296933,-1.63969850,-0.81321707,-0.04629182,
0.73721320,1.61278518,2.76647043,3.94804472)
x = data.frame(Raw.Score = Raw.Score, Severity = Severity)
Raw.score are raw numbers from 0 to 8 (let's consider them as the labels of the severity numbers)
Severity are relative numbres that represent the locations of the scores in the diagram
I want to graphically present the results as in the following example using ggplot (the example includes different numbers but I want something similar)
As a fun exercise in ggplot-ing here is one approach to achieve or come close to your desired result.
Raw.Score = c(0,1,2,3,4,5,6,7,8)
Severity = c(-3.56553994,-2.70296933,-1.63969850,-0.81321707,-0.04629182,
0.73721320,1.61278518,2.76647043,3.94804472)
dat <- data.frame(Raw.Score, Severity)
library(ggplot2)
dat_tile <- data.frame(
Severity = seq(-4.1, 4.1, .05)
)
dat_axis <- data.frame(
Severity = seq(-4, 4, 2)
)
tile_height = .15
ymax <- .5
ggplot(dat, aes(y = 0, x = Severity, fill = Severity)) +
# Axis line
geom_hline(yintercept = -tile_height / 2) +
# Colorbar
geom_tile(data = dat_tile, aes(color = Severity), height = tile_height) +
# Sgements connecting top and bottom labels
geom_segment(aes(xend = Severity, yend = -ymax, y = ymax), color = "orange") +
# Axis ticks aka dots
geom_point(data = dat_axis,
y = -tile_height / 2, shape = 21, stroke = 1, fill = "white") +
# ... and labels
geom_text(data = dat_axis, aes(label = Severity),
y = -tile_height / 2 - .1, vjust = 1, fontface = "bold") +
# Bottom labels
geom_label(aes(y = -ymax, label = scales::number(Severity, accuracy = .01))) +
# Top labels
geom_point(aes(y = ymax, color = Severity), size = 8) +
geom_text(aes(y = ymax, label = Raw.Score), fontface = "bold") +
# Colorbar annotations
annotate(geom = "text", fontface = "bold", label = "MILD", color = "black", x = -3.75, y = 0) +
annotate(geom = "text", fontface = "bold", label = "SEVERE", color = "white", x = 3.75, y = 0) +
# Fixing the scales
scale_x_continuous(expand = c(0, 0)) +
scale_y_continuous(limits = c(-ymax, ymax)) +
# Color gradient
scale_fill_gradient(low = "orange", high = "red", guide = "none") +
scale_color_gradient(low = "orange", high = "red", guide = "none") +
# Get rid of all non-data ink
theme_void() +
# Add some plot margin
theme(plot.margin = rep(unit(10, "pt"), 4)) +
coord_cartesian(clip = "off")
I have a bland-altman plot of 16 measurements divided over 3 groups (Slice) which I want to colorcode and possibly have different shapes but somehow I cant get it working:
df <- data.frame("Slice" = c(1,1,1,1,1,1,2,2,2,2,2,2,3,3,3,3),
"Segments" = c(1:16),
"mean" = c(6,5,2,4,8,9,6,3,5,6,5,8,5,4,6,4),
"dif" = c(1,3,2,1,2,3,2,1,2,2,2,1,3,2,1,2))
#creat limits of agreement
LL = mean(df$dif)-1.96*(sd(df$dif))
UL = mean(df$dif)+1.96*(sd(df$dif))
#create BA plot
BAplot <- ggplot(df, aes(x=mean,y=dif))+
geom_jitter(alpha=1.0,size=18,shape="*", stroke = 1.5)+
geom_hline(yintercept=mean(df$dif),color= "blue",size=2)+
geom_text(aes(x = 12, y = mean(df$dif)+0.2, label = round(mean(df$dif), 1)), col = "blue", size = 7) +
geom_hline(yintercept=0,linetype=3,size=2) +
geom_hline(yintercept=c(UL,LL),color="black",linetype="dashed",size=2)+theme_bw()+
geom_text(aes(x = 12, y = UL+0.2, label = round(UL,1)), col = "black", size = 7) +
geom_text(aes(x = 12, y = LL+0.2, label = round(LL,1)), col = "black", size = 7) +
scale_x_continuous("mean",limits = c(-2,12))+
scale_y_continuous("diff", limits = c(-1, 5.5))
To code your points by color and to have different shapes you have to map your Slice column on the color and/or shape aesthetic inside geom_jitter. As Slice is a numeric I first converted it to a factor. If you want specific colors or shape you could set your desired values using scale_color_manual and scale_shape_manual:
library(ggplot2)
ggplot(df, aes(x = mean, y = dif)) +
geom_jitter(aes(color = factor(Slice), shape = factor(Slice)), alpha = 1.0, size = 2) +
geom_hline(yintercept = mean(df$dif), color = "blue", size = 2) +
geom_text(aes(x = 12, y = mean(dif) + 0.2, label = round(mean(dif), 1)), col = "blue", size = 7) +
geom_hline(yintercept = 0, linetype = 3, size = 2) +
geom_hline(yintercept = c(UL, LL), color = "black", linetype = "dashed", size = 2) +
theme_bw() +
geom_text(aes(x = 12, y = UL + 0.2, label = round(UL, 1)), col = "black", size = 7) +
geom_text(aes(x = 12, y = LL + 0.2, label = round(LL, 1)), col = "black", size = 7) +
scale_x_continuous("mean", limits = c(-2, 12)) +
scale_y_continuous("diff", limits = c(-1, 5.5))
I am trying to reproduce this kind of Figure, with two densities, a first one pointing upwards and a second one pointing downwards. I would also like to have some blank space between the two densities.
Here is the code I am currently using.
library(hrbrthemes)
library(tidyverse)
library(RWiener)
# generating data
df <- rwiener(n = 1e2, alpha = 2, tau = 0.3, beta = 0.5, delta = 0.5)
df %>%
ggplot(aes(x = q) ) +
geom_density(
data = . %>% filter(resp == "upper"),
aes(y = ..density..),
colour = "steelblue", fill = "steelblue",
outline.type = "upper", alpha = 0.8, adjust = 1, trim = TRUE
) +
geom_density(
data = . %>% filter(resp == "lower"),
aes(y = -..density..), colour = "orangered", fill = "orangered",
outline.type = "upper", alpha = 0.8, adjust = 1, trim = TRUE
) +
# stimulus onset
geom_vline(xintercept = 0, lty = 1, col = "grey") +
annotate(
geom = "text",
x = 0, y = 0,
# hjust = 0,
vjust = -1,
size = 3, angle = 90,
label = "stimulus onset"
) +
# aesthetics
theme_ipsum_rc(base_size = 12) +
theme(axis.text.y = element_blank() ) +
labs(x = "Reaction time (in seconds)", y = "") +
xlim(0, NA)
Which results in something like...
How could I add some vertical space between the two densities to reproduce the above Figure?
If you want to try without faceting, you're probably best to just plot the densities as polygons with adjusted y values according to your desired spacing:
s <- 0.25 # set to change size of the space
ud <- density(df$q[df$resp == "upper"])
ld <- density(df$q[df$resp == "lower"])
x <- c(ud$x[1], ud$x, ud$x[length(ud$x)],
ld$x[1], ld$x, ld$x[length(ld$x)])
y <- c(s, ud$y + s, s, -s, -ld$y - s, -s)
df2 <- data.frame(x = x, y = y,
resp = rep(c("upper", "lower"), each = length(ud$x) + 2))
df2 %>%
ggplot(aes(x = x, y = y, fill = resp, color = resp) ) +
geom_polygon(alpha = 0.8) +
scale_fill_manual(values = c("steelblue", "orangered")) +
scale_color_manual(values = c("steelblue", "orangered"), guide = guide_none()) +
geom_vline(xintercept = 0, lty = 1, col = "grey") +
annotate(
geom = "text",
x = 0, y = 0,
# hjust = 0,
vjust = -1,
size = 3, angle = 90,
label = "stimulus onset"
) +
# aesthetics
theme_ipsum_rc(base_size = 12) +
theme(axis.text.y = element_blank() ) +
labs(x = "Reaction time (in seconds)", y = "")
you can try facetting
set.seed(123)
q=rbeta(100, 0.25, 1)
df_dens =data.frame(gr=1,
x=density(df$q)$x,
y=density(df$q)$y)
df_dens <- rbind(df_dens,
data.frame(gr=2,
x=density(df$q)$x,
y=-density(df$q)$y))
ggplot(df_dens, aes(x, y, fill = factor(gr))) +
scale_x_continuous(limits = c(0,1)) +
geom_area(show.legend = F) +
facet_wrap(~gr, nrow = 2, scales = "free_y") +
theme_minimal() +
theme(strip.background = element_blank(),
strip.text.x = element_blank(),
axis.text.y = element_blank(),
axis.title.y = element_blank())
The space between both plots can be increased using panel.spacing = unit(20, "mm"). Instead of facet_grid you can also try facet_grid(gr~., scales = "free_y")
I am trying to add different colors to a text in ggplot using the function annotate().
The results are quite good, but I have to define manually which are the right y values to correctly overlap the text.
Plot with annotations for
I would love to know if there is a better way to overlap text in annotations in R.
Thank you,
Btw, here is the code I am using:
ex_3_1 %>%
ggplot(aes(x = DATE)) +
# geometries
geom_line(aes(y = if_else(ORIGIN == "ACTUAL" |
(YEAR == 2019 & MONTH == "JUN"),
SALES, NULL)), size = 1) +
geom_line(aes(y = if_else(ORIGIN == "FORECAST", SALES, NULL)),
linetype = "dashed", size = 1) +
geom_point(aes(y = REL_SALES), size = 3) +
geom_point(aes(y = if_else(MONTH == "JUL" & YEAR == 2018, SALES, NULL)),
shape = 21, fill = "darkorange", size = 3) +
geom_point(aes(y = if_else(MONTH == "FEB" & YEAR == 2019, SALES, NULL)),
shape = 21, fill = col, size = 3) +
geom_text(aes(y = SALES, label = dollar(round(REL_SALES,1),
suffix = "B", accuracy = 0.1)),
vjust = -1.5, hjust = 0.2, size = 3) +
# annotations
# square text
annotate(geom = "rect", xmin = as_date("2019-05-20"),
xmax = as_date("2020-01-10"), ymin = 0, ymax = 2.6,
alpha = 0.1) +
annotate(geom = "text",
x = as_date("2020-01-01"), y = 1, hjust = 1, vjust = -1,
label = expression(bold("2019 FORECAST")),
col = "gray60", size = 3.25) +
annotate(geom = "text",
x = as_date("2020-01-01"), y = 1, hjust = 1, vjust = 1,
label = paste0("This is provided by ABC\n",
"consultants and based on\n",
"market data through June.\n",
"The forecast assumes no\n",
"major market changes.\n"),
col = "gray60", size = 3.5) +
# 2018 notes
annotate(
geom = "text", x = as_date("2018-01-10"), y = 3.5, hjust = 0, vjust = 1,
label = paste0("2018: Jan-Jun was a period of stability, with\n",
"fairly steady growth (averaging +3% per\n",
"month). There was a nearly 20% decrease\n",
"in July, when Product X was recalled and\n",
"pulled from the market. Total sales remained\n",
"at reduced volume for the rest of the year."),
col = "gray60", size = 3.5) +
annotate(
geom = "text", x = as_date("2018-01-10"), y = 3.5, hjust = 0, vjust = 1,
label = expression(bold("2018:")),
col = "gray60", size = 3.5) +
annotate(
geom = "text", x = as_date("2018-01-10"), y = 3.19, hjust = 0, vjust = 1,
label = expression(phantom("month). There was a ")*
"nearly 20% decrease"),
size = 3.5, col = "darkorange") +
annotate(
geom = "text", x = as_date("2018-01-10"), y = 3.03, hjust = 0, vjust = 1,
label = "in July",
size = 3.5, col = "darkorange") +
# 2019 notes
annotate(
geom = "text", x = as_date("2019-01-10"), y = 3.5, hjust = 0, vjust = 1,
label = paste0("2019: The year started at less than $1.6B, but\n",
"Increased markedly in February, when a new\n",
"study was released. Total sales have increased\n",
"steadly since then and this projected to continue.\n",
"The latest forecast is for $2.4B in monthly sales by\n",
"the end of the year."),
col = "gray60", size = 3.5) +
annotate(
geom = "text", x = as_date("2019-01-10"), y = 3.5, hjust = 0, vjust = 1,
label = expression(bold("2019:")),
col = "gray60", size = 3.5) +
annotate(
geom = "text", x = as_date("2019-01-10"), y = 3.35, hjust = 0, vjust = 1,
label = "Increased markedly in February",
size = 3.5, col = col) +
# scales
scale_x_date(date_labels = "%b'%y", date_breaks = "3 month") +
scale_y_continuous(labels = dollar, breaks = c(seq(0,3.5,0.5)),
limits = c(0, 3.5)) +
# titles
labs("Market size over time") +
ylab("SALES ($USD BILLIONS)") +
# themes
theme_void() +
theme(
axis.line.x = element_line(color = "gray58"),
axis.text.y = element_text(size = 11, color = "gray58"),
axis.title.y = element_text(hjust = 1, color = "gray58"),
axis.text.x = element_text(size = 9, color = "gray58")
)
I am attempting to recreate some plots from a research article in R and am running into an issue with applying a log scale to y axis. The visualization I'm attempting to recreate is this:
reference plot with y log scale
I currently have a working version without the logarithmic scale applied to the y-axis:
Proportion_Mean_Plot <- ggplot(proportions, aes(days2,
proportion_mean, group = observation)) +
geom_point(aes(shape = observation)) +
geom_line() +
scale_x_continuous(breaks = seq(0,335,20)) +
scale_y_continuous(breaks = seq(0,6,.5)) +
theme_tufte() +
geom_rangeframe() +
theme(legend.position="none") +
theme(axis.line.x = element_line(colour = "black", size = 0.5, linetype = 1),
axis.line.y = element_line(colour = "black", size = 0.5, linetype = 1)) +
labs(title = "Proportion of Baseline Mean",
subtitle = "Daily steps within each intervention phase",
x = "DAYS",
y = "PROPORTION OF BASELINE \n(MEAN)") +
geom_vline(xintercept = 164.5) +
geom_hline(yintercept = 1) +
annotate("text", x = c(82, 246), y = 5,
label = c("Intervention 1", "Intervention 2")) +
geom_segment(aes(x = 0, y = mean, xend = end, yend = mean),
data = proportion_intervention1_data) +
geom_segment(aes(x = start, y = mean, xend = end, yend = mean),
data = proportion_intervention2_data, linetype = 4)
This produces a decent representation of the original:
normally scaled y-axis plot
I would like to try to apply that logarithmic scaling to more closely match it. Any help is appreciated.
As per Richard's suggestion, here is a quick example how you can use scale_y_log10:
suppressPackageStartupMessages(library(tidyverse))
set.seed(123)
# generate some data
proportions <- tibble(interv_1 = pmax(0.4, rnorm(160, mean = 1.3, sd = 0.2)),
interv_2 = pmax(0.01, rnorm(160, mean = 1.6, sd = 0.5)))
proportions <- proportions %>%
gather(key = observation, value = proportion_mean) %>%
mutate(days2 = 1:320)
# create the plot
ggplot(proportions, aes(days2, proportion_mean, group = observation)) +
geom_point(aes(shape = observation)) +
geom_line() +
scale_x_continuous(breaks = seq(0,335,20), expand = c(0, 0)) +
scale_y_log10(breaks = c( 0.1, 0.5, 1, 2, 3, 4, 5), limits = c(0.1, 5)) +
# theme_tufte() +
# geom_rangeframe() +
theme(legend.position="none") +
theme(axis.line.x = element_line(colour = "black", size = 0.5, linetype = 1),
axis.line.y = element_line(colour = "black", size = 0.5, linetype = 1)) +
labs(title = "Proportion of Baseline Mean",
subtitle = "Daily steps within each intervention phase",
x = "DAYS",
y = "PROPORTION OF BASELINE \n(MEAN)") +
geom_vline(xintercept = 164.5) +
geom_hline(yintercept = 1) +
annotate("text", x = c(82, 246), y = 5,
label = c("Intervention 1", "Intervention 2")) +
# plugged the values for the means of the two distributions
geom_segment(aes(x = 0, y = 1.3, xend = 164.5, yend = 1.3)) +
geom_segment(aes(x = 164.5, y = 1.6, xend = 320, yend = 1.6), linetype = 4)