YuLab-SMU
can ggtreeExtra add errorbar for geom_bar
Yes, but the xmin or xmax mapping is not supported by ggtreeExtra. However, the geom_errorbar also can be added by controlling the stat parameters. You can refer to the following codes.
using geomExtra
library(ggtree)
library(ggtreeExtra)
library(ggplot2)
set.seed(1024)
tr <- rtree(10)
dat <- data.frame(id=rep(tr$tip.label, 5), value=abs(rnorm(50)))
df <- data.frame(id=rep(tr$tip.label), group=rep(c("A", "B", "C", "D", "E"), 2))
tr %<>% tidytree::left_join(dat, by=c("label"="id")) %>%
tidytree::left_join(df, by=c("label"="id"))
tr
p1 <- tr %>% ggtree() + geom_tiplab()
p2 <- p1 +
geom_fruit_list(
geom_fruit(
data = td_unnest(value),
geom = geom_bar,
mapping = aes(x = value, fill = group),
stat = "summary",
fun = mean,
orientation = "y",
position = position_identityx(), # This should be position_identidyx() for geom_bar in here.
pwidth = 3, # The pwidth and offset should be equal with geom_errorbar layer.
offset = 0.2
),
geom_fruit(
data = td_unnest(value),
geom = geom_errorbar,
mapping = aes(x = value, group = group),
stat = "summary",
fun.data = "mean_se",
orientation = "y",
position = position_identityx(),
width = 0.2,
pwidth = 3, # pwidth and offset should be equal with geom_bar.
offset = 0.2,
axis.params = list(axis="x", text.size = 3)
)
)
p2
# you can also use point to replace bar plot.
pp2 <- p1 +
geom_fruit_list(
geom_fruit(
data = td_unnest(value),
geom = geom_point,
mapping = aes(x = value, color = group),
stat = "summary",
fun = mean,
orientation = "y",
size = 3,
pwidth = 3, # The pwidth and offset should be equal with geom_errorbar layer.
offset = 0.2
),
geom_fruit(
data = td_unnest(value),
geom = geom_errorbar,
mapping = aes(x = value, group = group),
stat = "summary",
fun.data = "mean_se",
orientation = "y",
position = position_identityx(),
width = 0.2,
pwidth = 3, # pwidth and offset should be equal with geom_bar.
offset = 0.2,
axis.params = list(axis="x", text.size = 3)
)
)
pp2
You can also use geom_facet to display it when the layout of tree is not circular.
f2 <- p1 +
geom_facet(
data = td_unnest(value),
panel = "errorbar",
geom = geom_bar,
mapping = aes(x = value, fill = group),
stat = "summary",
fun = mean,
orientation = "y"
) +
geom_facet(
data = td_unnest(value),
panel = "errorbar",
geom = geom_errorbar,
mapping = aes(x = value, group = group),
stat = "summary",
fun.data = "mean_se",
orientation = "y",
width = 0.2
) +
theme_tree2()
f2
# Using point layer to replace bar plot
library(ggstar)
ff2 <- p1 +
geom_facet(
data = td_unnest(value),
panel = "errorbar",
geom = geom_star,
mapping = aes(x = value, fill = group),
stat = "summary",
fun = mean,
size = 3,
orientation = "y"
) +
geom_facet(
data = td_unnest(value),
panel = "errorbar",
geom = geom_errorbar,
mapping = aes(x = value, group = group),
stat = "summary",
fun.data = "mean_se",
orientation = "y",
width = 0.2
) +
theme_tree2()
ff2
Great Job. Thanks very much ! Best wishes to Yu LAB.
At 2021-09-16 20:54:43, "Shuangbin Xu" @.***> wrote:
Yes, but the xmin or xmax mapping is not supported by ggtreeExtra. However, the geom_errorbar also can be added by controlling the stat parameters. You can refer to the following codes.
using geomExtra library(ggtree) library(ggtreeExtra) library(ggplot2) set.seed(1024) tr <- rtree(10)
dat <- data.frame(id=rep(tr$tip.label, 5), value=abs(rnorm(50))) df <- data.frame(id=rep(tr$tip.label), group=rep(c("A", "B", "C", "D", "E"), 2)) tr %<>% tidytree::left_join(dat, by=c("label"="id")) %>% tidytree::left_join(df, by=c("label"="id")) tr p1 <- tr %>% ggtree() + geom_tiplab() p2 <- p1 + geom_fruit_list( geom_fruit( data = td_unnest(value), geom = geom_bar, mapping = aes(x = value, fill = group), stat = "summary", fun = mean, orientation = "y", position = position_identityx(), # This should be position_identidyx() for geom_bar in here. pwidth = 3, # The pwidth and offset should be equal with geom_errorbar layer. offset = 0.2 ), geom_fruit( data = td_unnest(value), geom = geom_errorbar, mapping = aes(x = value, group = group), stat = "summary", fun.data = "mean_se", orientation = "y", position = position_identityx(), width = 0.2, pwidth = 3, # pwidth and offset should be equal with geom_bar. offset = 0.2, axis.params = list(axis="x", text.size = 3) ) ) p2
you can also use point to replace bar plot.
pp2 <- p1 + geom_fruit_list( geom_fruit( data = td_unnest(value), geom = geom_point, mapping = aes(x = value, color = group), stat = "summary", fun = mean, orientation = "y", size = 3, pwidth = 3, # The pwidth and offset should be equal with geom_errorbar layer. offset = 0.2 ), geom_fruit( data = td_unnest(value), geom = geom_errorbar, mapping = aes(x = value, group = group), stat = "summary", fun.data = "mean_se", orientation = "y", position = position_identityx(), width = 0.2, pwidth = 3, # pwidth and offset should be equal with geom_bar. offset = 0.2, axis.params = list(axis="x", text.size = 3) ) ) pp2
You can also use geom_facet to display it when the layout of tree is not circular.
f2 <- p1 + geom_facet( data = td_unnest(value), panel = "errorbar", geom = geom_bar, mapping = aes(x = value, fill = group), stat = "summary", fun = mean, orientation = "y" ) + geom_facet( data = td_unnest(value), panel = "errorbar", geom = geom_errorbar, mapping = aes(x = value, group = group), stat = "summary", fun.data = "mean_se", orientation = "y", width = 0.2 ) + theme_tree2() f2
Using point layer to replace bar plot
library(ggstar) ff2 <- p1 + geom_facet( data = td_unnest(value), panel = "errorbar", geom = geom_star, mapping = aes(x = value, fill = group), stat = "summary", fun = mean, size = 3, orientation = "y" ) + geom_facet( data = td_unnest(value), panel = "errorbar", geom = geom_errorbar, mapping = aes(x = value, group = group), stat = "summary", fun.data = "mean_se", orientation = "y", width = 0.2 ) + theme_tree2() ff2
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