auto_ggenrich: Make enrichment factor plot.

In Hide-Fun/gglab: Make plots for research more simply

Description

Make enrichment factor plot. If you regulate more options, use ggenrich().

Usage

auto_ggenrich(
  .data,
  .data_ref,
  .mapping,
  .mapping_ref,
  .xlim,
  .ylim,
  .xlab = expression(paste(italic("ε"^{     13 }), "C", " (‰)")),
  .ylab = expression(paste(italic("ε"^{     15 }), "N", " (‰)")),
  .point_size = 3,
  .stroke = 0.82,
  .shape_val = c(16, 17, 24),
  .cross_tip = 0.15,
  .linesize = 0.55,
  .axis_size = 0.55,
  .linetype = "dashed",
  .hjust = 0,
  .vjust = 0,
  .x_breaks = scales::breaks_extended(6),
  .y_breaks = scales::breaks_extended(6),
  .family = "Arial",
  .label_size = 4,
  .lab_title_size = 15,
  .lab_text_size = 12,
  .ratio = 2/3,
  .multi = F,
  .scaling = F,
  .scale_var = NULL,
  ...
)

Arguments

.data	data.
.data_ref	data of reference autotrophic plants.
.mapping	mapping, wrapping by aes(), augments passing through geom_***.
.mapping_ref	mapping, reference data set.
.xlim	range of x axis.
.ylim	range of y axis.
.xlab	title of x axis.
.ylab	title of y axis.
.point_size	size of point.
.stroke	edge of point
.shape_val	shape of point, passing scale_shape_manual().
.cross_tip	width and height of errorbar.
.linesize	width of line in error bar.
.linetype	dashed or dotted and so on.
.hjust	place of label (horizontal).
.vjust	place of label (vertical).
.x_breaks	break of x.
.y_breaks	break of y.
.family	font family, default Arial.
.label_size	label size.
.lab_title_size	axis title.
.lab_text_size	axis text
.ratio	ratio of plot.
.multi	logical
.scaling	logical
.scale_var	numeric
...	passed through theme().

Examples

library(ggplot2)
library(dplyr)
library(stringr)

data("demo")

# summarise data.
by_place <- demo %>%
  group_by(place, label) %>%
  summarise(across(where(is.numeric),
                   list(mean = mean, sd = sd),
                   .names = "{.fn}_{.col}")) %>%
  filter(place == "A")

# select "place is A".
val <- by_place %>%
  filter(str_detect(label, "target"))

# reference data.
ref <- by_place %>%
 filter(str_detect(label, "ref"))

# make plot (default).
auto_ggenrich(.data = val,
              .data_ref = ref,
              .mapping = aes(x = mean_epsilon13C, y = mean_epsilon15N,
                             xmin = mean_epsilon13C - sd_epsilon13C,
                             xmax = mean_epsilon13C + sd_epsilon13C,
                             ymin = mean_epsilon15N - sd_epsilon15N,
                             ymax = mean_epsilon15N + sd_epsilon15N,
                             shape = label,
                             label = label),
              .mapping_ref = aes(xmin = mean_epsilon13C - sd_epsilon13C,
                                 xmax = mean_epsilon13C + sd_epsilon13C,
                                 ymin = mean_epsilon15N - sd_epsilon15N,
                                 ymax = mean_epsilon15N + sd_epsilon15N),
              .xlim = c(-5, 3),
              .ylim = c(-3, 5),
              .family = NULL,
              .x_breaks = seq(-5, 3, 1),
              .y_breaks = seq(-3, 5, 1))

# make plot (manual).
auto_ggenrich(.data = val,
              .data_ref = ref,
              .mapping = aes(x = mean_epsilon13C, y = mean_epsilon15N,
                             xmin = mean_epsilon13C - sd_epsilon13C,
                             xmax = mean_epsilon13C + sd_epsilon13C,
                             ymin = mean_epsilon15N - sd_epsilon15N,
                             ymax = mean_epsilon15N + sd_epsilon15N,
                             shape = label,
                             label = label),
              .mapping_ref = aes(xmin = mean_epsilon13C - sd_epsilon13C,
                                 xmax = mean_epsilon13C + sd_epsilon13C,
                                 ymin = mean_epsilon15N - sd_epsilon15N,
                                 ymax = mean_epsilon15N + sd_epsilon15N),
              .xlim = c(-5, 3),
              .ylim = c(-3, 5),
              .xlab = expression(paste(italic("δ"^{13}), "C", " (\u2030)")),
              .ylab = expression(paste(italic("δ"^{15}), "N", " (\u2030)")),
              .hjust = 0, .vjust = 0,
              .cross_tip = .3,
              .stroke = 1,
              .linesize = .8,
              .axis_size = .8,
              .shape_val = c(24, 21, 16, 23),
              .x_breaks = scales::breaks_extended(6),
              .y_breaks = scales::breaks_extended(6),
              .family = NULL,
              .lab_title_size = 15,
              .lab_text_size = 12,
              .label_size = 4,
              .point_size = 3,
              .ratio = 1/2,
              .multi = F)

Hide-Fun/gglab documentation built on Dec. 31, 2020, 1 p.m.