使用 coord_fixed 后从 ggplot 中删除空 space
Removing empty space from ggplot after coord_fixed is used
我正在尝试将三个不同的地块绘制在一起以形成一个更大的图。问题是 plot.margin(c(0,0,0,0), "cm") 没有按预期删除空格。如果我删除 coord_fixed.
，这些数字会按预期靠在一起
示例数据集、生成数据集的代码以及用于生成示例的代码。
数据集代码。
library(tidyverse)
library(cowplot)
n_pat <- 25
patient <- 1:n_pat
censoring <- ceil(rexp(n_pat, 1/30))
tumour_shrink <- (rbeta(n_pat, 2, 2) - 0.5) * 100
n_params <- 15
parameters <- paste("Parameter", 1:n_params)
response <- sample(c("PR", "NE", "CR", "PD", "SD"), size=n_pat,
replace = T)
missing_combination <- sample(c(TRUE, FALSE), size=n_pat, replace=T)
changes <- matrix(runif(n_pat * n_params, 1, 100), nrow=n_pat, ncol=n_cytokines)
changes[sample(1:dim(changes)[1], 4, replace = FALSE), sample(1:dim(changes)[2], 5, replace = F)] <- NA
df <- data.frame(patient, censoring, tumour_shrink, changes, missing_combination)
colnames(df) <- c("patient", "censoring", "tumour_shrink", cytokines, "missing_combination")
地块代码：
p1 <- df %>%
mutate(color = case_when(
response == "PR" ~ "lightgreen",
response == "NE" ~ "white",
response == "CR" ~ "darkgreen",
response == "PD" ~ "red",
response == "SD" ~ "yellow"
)) %>%
arrange(tumour_shrink) %>%
mutate(patient = factor(patient, levels=patient)) %>%
ggplot(aes(x=patient, y=1, fill=color)) +
geom_raster() +
coord_fixed() +
geom_tile(color="black", size=1) +
geom_text(aes(label=response), size=3) +
theme(axis.text = element_blank(),
axis.ticks = element_blank(),
legend.position = "none",
axis.ticks.length = unit(0, "mm"),
axis.title.y = element_text(angle = 0, vjust=0.57, size = 12),
plot.margin = unit(c(0, 0, 0, 0), "cm")) +
scale_fill_identity() +
labs(y="Best ov. resp", x=NULL)
p2 <- df %>%
arrange(tumour_shrink) %>%
mutate(patient = factor(patient, levels=patient)) %>%
mutate(color = ifelse(missing_combination, "white", "gray")) %>%
ggplot(aes(x=patient, y=1, fill=color)) +
geom_raster() +
geom_tile(color="black", size=1) +
geom_text(aes(label=censoring), size=3) +
scale_fill_identity() +
labs(y="Censoring", x=NULL) +
coord_fixed() +
theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "mm"),
legend.position = "none",
axis.title.y = element_text(angle = 0, vjust=0.57, size=12),
plot.margin = unit(c(0, 0, 0, 0), "pt"))
p3 <- df %>%
arrange(tumour_shrink) %>%
mutate(patient = factor(patient, levels=patient)) %>%
ggplot(aes(x=factor(patient), y=1, fill=tumour_shrink)) +
geom_raster(alpha=0.8) +
geom_tile(color="black", size=1) +
coord_fixed() +
geom_text(aes(label=formatC(tumour_shrink, 0, format="f")),
size=3) +
theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "mm"),
axis.title.y = element_text(angle = 0, vjust=0.57, size=12),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
legend.position = "none") +
scale_fill_gradient(low="green", high="red") +
labs(y="Tumour shrink", x=NULL)
plot_grid(p1, p2, p3, ncol=1, align="v", axis="lr")
patchwork 包提供了一个简单的解决方案：
library(patchwork)
wrap_plots(p1, p2, p3, ncol=1)
另一种选择：将所有内容绘制在一个图中。这样做的好处是您可以完全控制间距，并且减少了对 cowplot/patchwork.
的需求
这需要对您的绘图方法进行一些更改：
- 为每一行定义不同的
color，facilitated/enabled 通过使用 scale_fill_identity;
- 每个几何体分开
y=；
- 使用
rank(-tumour_shrink) 作为 x 值而不是 patient;
- 删除
axis.ticks 主题，因为我（滥用）将它们用于“审查”（等）y 轴标签（并手动分配这些标签）；和
- 添加更多主题元素以移除背景网格。
为了可重复性，我将ceil替换为ceiling，并设置了随机种子：
set.seed(42)
# df <- ...
head(df)
# patient censoring tumour_shrink Cytokine 1 Cytokine 2 Cytokine 3 Cytokine 4 Cytokine 5
# 1 1 6 -4.554208 45.73676 78.626829 57.88910 56.582358 87.05652
# 2 2 20 42.752870 32.38828 13.758344 35.98169 8.001468 21.29991
# 3 3 9 10.031523 NA 13.779839 55.19518 NA NA
# 4 4 2 8.484090 19.42411 8.153058 89.37914 55.412421 88.78861
# 5 5 15 -11.012928 73.24328 6.259819 49.50907 48.716163 14.49329
# 6 6 44 21.390972 41.77534 53.655569 17.99158 16.787516 78.74959
# Cytokine 6 Cytokine 7 Cytokine 8 Cytokine 9 Cytokine 10 Cytokine 11 Cytokine 12 Cytokine 13
# 1 73.439052 30.38779 10.000912 61.971232 52.95427 26.663044 92.21165 32.736054
# 2 32.210819 65.66861 80.061067 92.588889 66.02428 78.010740 36.89758 19.686203
# 3 39.258947 90.20598 NA 39.612267 NA 43.220164 85.65836 39.989134
# 4 33.912153 99.08878 5.008270 29.504049 72.40138 6.944785 30.78971 86.340576
# 5 9.888019 43.60299 5.067548 9.982861 49.58429 12.368421 47.10058 35.443229
# 6 75.948505 39.98392 95.488990 32.881356 96.56030 48.792933 15.13034 1.141956
# Cytokine 14 Cytokine 15 missing_combination
# 1 48.93261 16.28906 TRUE
# 2 84.69391 27.37059 FALSE
# 3 42.21307 35.72471 TRUE
# 4 49.44491 58.26738 TRUE
# 5 19.14549 81.05158 TRUE
# 6 76.15699 93.39376 FALSE
我任意使用 1、3 和 5 作为 y 值，您显然可以更改它们以满足您的需要。
library(dplyr)
library(ggplot2)
df %>%
arrange(tumour_shrink) %>%
mutate(
xval = rank(-tumour_shrink),
patient = factor(patient),
color1 = case_when(
response == "PR" ~ "lightgreen",
response == "NE" ~ "white",
response == "CR" ~ "darkgreen",
response == "PD" ~ "red",
response == "SD" ~ "yellow"
),
color2 = if_else(missing_combination, "white", "gray"),
color3 = do.call(rgb, asplit(colorRamp(colors = c("green", "red"))(
(tumour_shrink - min(tumour_shrink)) / diff(range(tumour_shrink))
)/255, 2))
) %>%
ggplot(aes(x = xval)) +
coord_fixed() +
# plot 1
geom_tile(aes(y = 5, fill = color1), color="black") +
geom_text(aes(y = 5, label = response), size=3) +
# plot 2
geom_tile(aes(y = 3, fill=color2), color="black") +
geom_text(aes(y = 3, label=response), size=3) +
# plot 3
geom_tile(aes(y = 1, fill = color3), color = "black") +
geom_text(aes(y = 1, label = formatC(tumour_shrink, 0, format="f")),
size=3) +
theme(
legend.position = "none",
axis.ticks.length = unit(0, "mm"),
axis.title.y = element_text(angle = 0, vjust=0.57, size = 12),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
scale_fill_identity() +
scale_y_continuous(
name = NULL, breaks = c(5,3,1),
labels = c("Best ov. resp", "Censoring", "Tumour shrink")) +
scale_x_discrete(name = NULL)
我承认 do.call(rgb, ...) 有点过头了，但它提供了相同的效果，而且我从来没有真正喜欢过矩阵 return - [=23 的值=]. （同样，该部分是通过使用 scale_fill_identity 启用的，没有它就不会是 easy/feasible。）
我正在尝试将三个不同的地块绘制在一起以形成一个更大的图。问题是 plot.margin(c(0,0,0,0), "cm") 没有按预期删除空格。如果我删除 coord_fixed.
，这些数字会按预期靠在一起示例数据集、生成数据集的代码以及用于生成示例的代码。
数据集代码。
library(tidyverse)
library(cowplot)
n_pat <- 25
patient <- 1:n_pat
censoring <- ceil(rexp(n_pat, 1/30))
tumour_shrink <- (rbeta(n_pat, 2, 2) - 0.5) * 100
n_params <- 15
parameters <- paste("Parameter", 1:n_params)
response <- sample(c("PR", "NE", "CR", "PD", "SD"), size=n_pat,
replace = T)
missing_combination <- sample(c(TRUE, FALSE), size=n_pat, replace=T)
changes <- matrix(runif(n_pat * n_params, 1, 100), nrow=n_pat, ncol=n_cytokines)
changes[sample(1:dim(changes)[1], 4, replace = FALSE), sample(1:dim(changes)[2], 5, replace = F)] <- NA
df <- data.frame(patient, censoring, tumour_shrink, changes, missing_combination)
colnames(df) <- c("patient", "censoring", "tumour_shrink", cytokines, "missing_combination")
地块代码：
p1 <- df %>%
mutate(color = case_when(
response == "PR" ~ "lightgreen",
response == "NE" ~ "white",
response == "CR" ~ "darkgreen",
response == "PD" ~ "red",
response == "SD" ~ "yellow"
)) %>%
arrange(tumour_shrink) %>%
mutate(patient = factor(patient, levels=patient)) %>%
ggplot(aes(x=patient, y=1, fill=color)) +
geom_raster() +
coord_fixed() +
geom_tile(color="black", size=1) +
geom_text(aes(label=response), size=3) +
theme(axis.text = element_blank(),
axis.ticks = element_blank(),
legend.position = "none",
axis.ticks.length = unit(0, "mm"),
axis.title.y = element_text(angle = 0, vjust=0.57, size = 12),
plot.margin = unit(c(0, 0, 0, 0), "cm")) +
scale_fill_identity() +
labs(y="Best ov. resp", x=NULL)
p2 <- df %>%
arrange(tumour_shrink) %>%
mutate(patient = factor(patient, levels=patient)) %>%
mutate(color = ifelse(missing_combination, "white", "gray")) %>%
ggplot(aes(x=patient, y=1, fill=color)) +
geom_raster() +
geom_tile(color="black", size=1) +
geom_text(aes(label=censoring), size=3) +
scale_fill_identity() +
labs(y="Censoring", x=NULL) +
coord_fixed() +
theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "mm"),
legend.position = "none",
axis.title.y = element_text(angle = 0, vjust=0.57, size=12),
plot.margin = unit(c(0, 0, 0, 0), "pt"))
p3 <- df %>%
arrange(tumour_shrink) %>%
mutate(patient = factor(patient, levels=patient)) %>%
ggplot(aes(x=factor(patient), y=1, fill=tumour_shrink)) +
geom_raster(alpha=0.8) +
geom_tile(color="black", size=1) +
coord_fixed() +
geom_text(aes(label=formatC(tumour_shrink, 0, format="f")),
size=3) +
theme(axis.text = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank(),
axis.ticks.length = unit(0, "mm"),
axis.title.y = element_text(angle = 0, vjust=0.57, size=12),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
legend.position = "none") +
scale_fill_gradient(low="green", high="red") +
labs(y="Tumour shrink", x=NULL)
plot_grid(p1, p2, p3, ncol=1, align="v", axis="lr")
patchwork 包提供了一个简单的解决方案：
library(patchwork)
wrap_plots(p1, p2, p3, ncol=1)
另一种选择：将所有内容绘制在一个图中。这样做的好处是您可以完全控制间距，并且减少了对 cowplot/patchwork.
这需要对您的绘图方法进行一些更改：
- 为每一行定义不同的
color，facilitated/enabled 通过使用scale_fill_identity; - 每个几何体分开
y=； - 使用
rank(-tumour_shrink)作为 x 值而不是patient; - 删除
axis.ticks主题，因为我（滥用）将它们用于“审查”（等）y 轴标签（并手动分配这些标签）；和 - 添加更多主题元素以移除背景网格。
为了可重复性，我将ceil替换为ceiling，并设置了随机种子：
set.seed(42)
# df <- ...
head(df)
# patient censoring tumour_shrink Cytokine 1 Cytokine 2 Cytokine 3 Cytokine 4 Cytokine 5
# 1 1 6 -4.554208 45.73676 78.626829 57.88910 56.582358 87.05652
# 2 2 20 42.752870 32.38828 13.758344 35.98169 8.001468 21.29991
# 3 3 9 10.031523 NA 13.779839 55.19518 NA NA
# 4 4 2 8.484090 19.42411 8.153058 89.37914 55.412421 88.78861
# 5 5 15 -11.012928 73.24328 6.259819 49.50907 48.716163 14.49329
# 6 6 44 21.390972 41.77534 53.655569 17.99158 16.787516 78.74959
# Cytokine 6 Cytokine 7 Cytokine 8 Cytokine 9 Cytokine 10 Cytokine 11 Cytokine 12 Cytokine 13
# 1 73.439052 30.38779 10.000912 61.971232 52.95427 26.663044 92.21165 32.736054
# 2 32.210819 65.66861 80.061067 92.588889 66.02428 78.010740 36.89758 19.686203
# 3 39.258947 90.20598 NA 39.612267 NA 43.220164 85.65836 39.989134
# 4 33.912153 99.08878 5.008270 29.504049 72.40138 6.944785 30.78971 86.340576
# 5 9.888019 43.60299 5.067548 9.982861 49.58429 12.368421 47.10058 35.443229
# 6 75.948505 39.98392 95.488990 32.881356 96.56030 48.792933 15.13034 1.141956
# Cytokine 14 Cytokine 15 missing_combination
# 1 48.93261 16.28906 TRUE
# 2 84.69391 27.37059 FALSE
# 3 42.21307 35.72471 TRUE
# 4 49.44491 58.26738 TRUE
# 5 19.14549 81.05158 TRUE
# 6 76.15699 93.39376 FALSE
我任意使用 1、3 和 5 作为 y 值，您显然可以更改它们以满足您的需要。
library(dplyr)
library(ggplot2)
df %>%
arrange(tumour_shrink) %>%
mutate(
xval = rank(-tumour_shrink),
patient = factor(patient),
color1 = case_when(
response == "PR" ~ "lightgreen",
response == "NE" ~ "white",
response == "CR" ~ "darkgreen",
response == "PD" ~ "red",
response == "SD" ~ "yellow"
),
color2 = if_else(missing_combination, "white", "gray"),
color3 = do.call(rgb, asplit(colorRamp(colors = c("green", "red"))(
(tumour_shrink - min(tumour_shrink)) / diff(range(tumour_shrink))
)/255, 2))
) %>%
ggplot(aes(x = xval)) +
coord_fixed() +
# plot 1
geom_tile(aes(y = 5, fill = color1), color="black") +
geom_text(aes(y = 5, label = response), size=3) +
# plot 2
geom_tile(aes(y = 3, fill=color2), color="black") +
geom_text(aes(y = 3, label=response), size=3) +
# plot 3
geom_tile(aes(y = 1, fill = color3), color = "black") +
geom_text(aes(y = 1, label = formatC(tumour_shrink, 0, format="f")),
size=3) +
theme(
legend.position = "none",
axis.ticks.length = unit(0, "mm"),
axis.title.y = element_text(angle = 0, vjust=0.57, size = 12),
plot.margin = unit(c(0, 0, 0, 0), "cm"),
panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +
scale_fill_identity() +
scale_y_continuous(
name = NULL, breaks = c(5,3,1),
labels = c("Best ov. resp", "Censoring", "Tumour shrink")) +
scale_x_discrete(name = NULL)
我承认 do.call(rgb, ...) 有点过头了，但它提供了相同的效果，而且我从来没有真正喜欢过矩阵 return - [=23 的值=]. （同样，该部分是通过使用 scale_fill_identity 启用的，没有它就不会是 easy/feasible。）