Chapter 2 ggplot主题使用
2.1 ggplot作图字体及线条单位
pointsize 是绘图点大小，单位是 1/72 英寸，一般情况下不会修改pointsize大小。
1 in = 25.4mm = 72.27points，1mm = 2.845276 points
1 mm = .pt = 2.845276 points .pt为R语言作图的最小单位。
ggplot2函数用法规定: 字体单位为pt, 线条单位为mm.
library(ggplot2)
.pt## [1] 2.845276#设置1.5pt线宽, ggplot2中线条宽度单位为mm
lwd = 1.5/.pt
lwd## [1] 0.52718972.2 theme_grey默认参数
theme_grey的默认参数, 包含了theme所有的默认设定, 可以帮助理解ggplot的theme参数.
# ggplot默认主题及默认参数
theme_grey <- function (base_size = 11, base_family = "", base_line_size = base_size/22, base_rect_size = base_size/22) {
half_line <- base_size/2
t <- theme(line = element_line(colour = "black", size = base_line_size, linetype = 1, lineend = "butt"),
rect = element_rect(fill = "white", colour = "black", size = base_rect_size, linetype = 1),
text = element_text(family = base_family, face = "plain", colour = "black", size = base_size, lineheight = 0.9, hjust = 0.5, vjust = 0.5, angle = 0, margin = margin(), debug = FALSE),
axis.line = element_blank(),
axis.line.x = NULL,
axis.line.y = NULL,
axis.text = element_text(size = rel(0.8), colour = "grey30"),
axis.text.x = element_text(margin = margin(t = 0.8 * half_line/2), vjust = 1),
axis.text.x.top = element_text(margin = margin(b = 0.8 * half_line/2), vjust = 0),
axis.text.y = element_text(margin = margin(r = 0.8 * half_line/2), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = 0.8 * half_line/2), hjust = 0),
axis.ticks = element_line(colour = "grey20"),
axis.ticks.length = unit(half_line/2, "pt"), axis.ticks.length.x = NULL,
axis.ticks.length.x.top = NULL, axis.ticks.length.x.bottom = NULL,
axis.ticks.length.y = NULL, axis.ticks.length.y.left = NULL,
axis.ticks.length.y.right = NULL,
axis.title.x = element_text(margin = margin(t = half_line/2), vjust = 1),
axis.title.x.top = element_text(margin = margin(b = half_line/2), vjust = 0),
axis.title.y = element_text(angle = 90, margin = margin(r = half_line/2), vjust = 1),
axis.title.y.right = element_text(angle = -90, margin = margin(l = half_line/2), vjust = 0),
legend.background = element_rect(colour = NA),
legend.spacing = unit(2 * half_line, "pt"),
legend.spacing.x = NULL,
legend.spacing.y = NULL,
legend.margin = margin(half_line, half_line, half_line, half_line),
legend.key = element_rect(fill = "grey95", colour = NA),
legend.key.size = unit(1.2, "lines"),
legend.key.height = NULL,
legend.key.width = NULL,
legend.text = element_text(size = rel(0.8)),
legend.text.align = NULL,
legend.title = element_text(hjust = 0),
legend.title.align = NULL,
legend.position = "right",
legend.direction = NULL,
legend.justification = "center",
legend.box = NULL,
legend.box.margin = margin(0, 0, 0, 0, "cm"),
legend.box.background = element_blank(),
legend.box.spacing = unit(2 * half_line, "pt"),
panel.background = element_rect(fill = "grey92", colour = NA),
panel.border = element_blank(),
panel.grid = element_line(colour = "white"),
panel.grid.minor = element_line(size = rel(0.5)),
panel.spacing = unit(half_line, "pt"),
panel.spacing.x = NULL,
panel.spacing.y = NULL,
panel.ontop = FALSE,
strip.background = element_rect(fill = "grey85", colour = NA),
strip.text = element_text(colour = "grey10", size = rel(0.8),
margin = margin(0.8 * half_line, 0.8 * half_line, 0.8 * half_line, 0.8 * half_line)),
strip.text.x = NULL, strip.text.y = element_text(angle = -90),
strip.text.y.left = element_text(angle = 90),
strip.placement = "inside",
strip.placement.x = NULL,
strip.placement.y = NULL,
strip.switch.pad.grid = unit(half_line/2, "pt"),
strip.switch.pad.wrap = unit(half_line/2, "pt"),
plot.background = element_rect(colour = "white"),
plot.title = element_text(size = rel(1.2), hjust = 0, vjust = 1, margin = margin(b = half_line)),
plot.title.position = "panel",
plot.subtitle = element_text(hjust = 0, vjust = 1, margin = margin(b = half_line)),
plot.caption = element_text(size = rel(0.8), hjust = 1, vjust = 1, margin = margin(t = half_line)),
plot.caption.position = "panel",
plot.tag = element_text(size = rel(1.2), hjust = 0.5, vjust = 0.5),
plot.tag.position = "topleft",
plot.margin = margin(half_line, half_line, half_line, half_line), complete = TRUE)
ggplot_global$theme_all_null %+replace% t
}2.3 theme_bw默认参数
- 修改默认字体大小, 默认线条粗细, 默认边框粗细.
- 去除作图背景颜色.(原有背景为灰色)
- 调整主坐标轴, 次坐标轴线条颜色为
grey92; 次坐标轴线体修改为原来的一半. - 调整图例的背景为白色.
为什么选择theme_bw主题, 是因为paper发表文章, theme_bw经过修改之后比较简洁.
# ggplot theme_bw主题调节内容
theme_bw <- function (base_size = 11, base_family = "", base_line_size = base_size/22, base_rect_size = base_size/22) {
theme_grey(base_size = base_size,
base_family = base_family,
base_line_size = base_line_size, base_rect_size = base_rect_size) %+replace%
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "grey20"),
panel.grid = element_line(colour = "grey92"),
panel.grid.minor = element_line(size = rel(0.5)),
strip.background = element_rect(fill = "grey85", colour = "grey20"),
legend.key = element_rect(fill = "white", colour = NA), complete = TRUE)
}2.4 theme_bw主题修改
- 坐标轴字体调整为黑色;
- 坐标轴线调整为黑色
ggplot2函数用法规定: base_size单位为pt, base_line_size和base_rect_size单位为mm.
文章发表字体大小6-12pt, 线条粗细0.5pt ~ 1.5pt, 由于线条单位默认为mm,因此要除以.pt
theme_bw1 <- function (base_size = 11, base_family = "", base_line_size = base_size/22, base_rect_size = base_size/22)
{
theme_grey(base_size = base_size,
base_family = base_family,
base_line_size = base_line_size, base_rect_size = base_rect_size) %+replace%
theme(panel.background = element_rect(fill = "white", colour = NA),
panel.border = element_rect(fill = NA, colour = "black"),
panel.grid = element_line(colour = "grey92"),
panel.grid.minor = element_line(size = rel(0.5)),
strip.background = element_rect(fill = "grey85", colour = "grey20"),
legend.key = element_rect(fill = "white", colour = NA), complete = TRUE,
axis.text = element_text(size = rel(0.8), colour = "black"), )
}
p + theme_bw1(base_size = 12,base_line_size = 1.5/.pt,base_rect_size = 1.5/.pt)2.5 Figure 保存技巧
在Rstudio的Plots Panel或R语言中调节合适的figure大小，Rstudio默认输出的图片dpi为96，因此显示的(像素大小/96)即为图片的物理尺寸，我们可以根据右侧图片中字体大小，线条粗细和绘图区点等的大小实时调整，调整完后，设置高度及宽度，示例如下：
ggsave("test.png", g, width = 579/96, height =304/96,units = "in",dpi=300)
#578, 304为在Rstudio中显示图片的分辨率; 96为dpi, 比值为物理尺寸大小"in"， 一般paper要求ppi高于300。2.6 参考
https://www.cnblogs.com/lmj-sky/p/13353197.html
https://zhuanlan.zhihu.com/p/344015507
https://www.jianshu.com/p/054107c7aac3
https://www.aohuiliu.fun/posts/44687/
2.7 包版本
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggplot2_3.3.6
##
## loaded via a namespace (and not attached):
## [1] bslib_0.4.0 compiler_3.6.3 pillar_1.8.1 jquerylib_0.1.4
## [5] tools_3.6.3 digest_0.6.29 jsonlite_1.8.0 evaluate_0.16
## [9] lifecycle_1.0.1 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3
## [13] rlang_1.1.0 DBI_1.1.3 cli_3.4.1 rstudioapi_0.14
## [17] yaml_2.3.5 xfun_0.33 fastmap_1.1.0 withr_2.5.0
## [21] stringr_1.4.1 dplyr_1.0.10 knitr_1.40 generics_0.1.3
## [25] sass_0.4.2 vctrs_0.4.1 tidyselect_1.1.2 grid_3.6.3
## [29] glue_1.6.2 R6_2.5.1 fansi_1.0.3 rmarkdown_2.16
## [33] bookdown_0.30 purrr_0.3.4 magrittr_2.0.3 scales_1.2.1
## [37] htmltools_0.5.3 assertthat_0.2.1 colorspace_2.0-3 utf8_1.2.2
## [41] stringi_1.7.8 munsell_0.5.0 cachem_1.0.6