ggcorr: Plot scatterplot with correlation coefficients and ab-line...

In SATVILab/UtilsGGSV: Utility functions for ggplot2

Plot scatterplot with correlation coefficients and ab-line overlaid

Description

Plots a scatterplot with various correlation coefficients and an optional ab-line overlaid.

Usage

ggcorr(
  data,
  corr_method = "spearman",
  corr_lab = "auto",
  grp,
  grp_base = NULL,
  grp_x = NULL,
  grp_lab = "auto",
  y,
  id,
  est_signif = 3,
  ci = TRUE,
  pval = TRUE,
  ci_signif = 3,
  pval_signif = 3,
  pval_trunc = 0.001,
  label_id = FALSE,
  label_id_size = 3,
  trans = "identity",
  coord = c(0.05, 0.95),
  skip = 0.05,
  font_size = 4.2,
  hjust = 0,
  vjust = 0.5,
  point_size = 1,
  point_alpha = 0.9,
  limits_expand = NULL,
  limits_equal = FALSE,
  legend_title = FALSE,
  legend_position = "bottom",
  thm = cowplot::theme_cowplot() + theme(plot.background = element_rect(fill = "white")),
  grid = cowplot::background_grid(major = "xy"),
  grp_to_col = NULL,
  abline = FALSE,
  smooth = TRUE,
  smooth_method = "lm",
  smooth_se = FALSE
)

Arguments

data	dataframe. Dataframe containing the data to be plotted.
corr_method	character vector. Correlation method. One or more of c("concordance", "pearson", "spearman", "kendall"). Default is "spearman".
corr_lab	⁠"never"``, ⁠"auto"“, "always" or a named character vector. Whether, and how, to label the correlation methods in the plot. If "always" or "never", then the correlation labels are always or never displayed, respectively. If '"auto"', then they are displayed only if multiple correlation methods are used. If displaye dusing '"always"' or '"never"', then default labels are used. If a named character vector, then the names are the correlation methods and the values are the labels, e.g. 'c("spearman" = "Spearman", "kendall" = "Kendall")'. Default is '"auto"'. correlation methods are used.
grp	character. Name of the column in data that specifies the variables to compare between. The first level within grp (i.e. data[[grp]][1]) is the level plotted on the x-axis, unless grp_x is set (see below).
grp_base	character. If not NULL, then only correlations between this level within data[[grp]] and other levels are displayed. If NULL, all two-way correlations are displayed. Default is NULL.
grp_x	character. If NULL, then this level of grp is plotted along the x-axis. Default is NULL.
grp_lab	"always", "auto" or "never". Whether to label the groups being compared for a specific displayed correlation coefficients. If "always" or "never", then the groups are always or never labelled, respectively. If "auto", then the groups are labelled only if multiple groups are compared. Default is "auto".
y	character. Name of the column in data that specifies the values being correlated between groups.
id	character. Name of the column in data that specifies the subject from which multiple measurements were taken.
est_signif	numeric. Significant digits for correlation estimates. Default is 3.
ci	logical. Whether to include confidence intervals for correlation estimates. Default is TRUE.
pval	logical. Whether to include p-values for correlation estimates. Default is TRUE.
ci_signif	numeric. Significant digits for confidence intervals. Default is 3.
pval_signif	numeric. Significant digits for p-values. Default is 3.
pval_trunc	numeric. P-values smaller than this threshold will be displayed as "< threshold". Default is 0.001.
label_id	logical. If TRUE, points labels as given by data[[id]] are displayed using ggrepel::geom_text_repel. Default is FALSE.
label_id_size	numeric. Size of labels. Default is 3.
trans	character or trans object. Specifies scaling of y- and x-axes. If class is character, it is converted to a trans object. Adds "root_cube", "root_fourth", "root_fifth" and "asinh" transformations, as well as "sqrt" transformation that allows plotting of lines at zero. If class is a trans object, it is returned as is. Default is "identity".
coord	numeric vector. Coordinates for text placement for first (or only) row of results. Specified in terms of proportion of axis length, with the first value specifying the x-axis coordinate and the second value the y-axis coordinate. Default is c(0.05, 0.95), which places the first row in the top left corner of the plot.
skip	numeric. Proportion of y-axis to move down between lines of text. Default is 0.05.
font_size	numeric. Font size for text in results table. Default is 10.
hjust	numeric. Horizontal justification for text. Default is 0.
vjust	numeric. Vertical justification for text. Default is 0.5.
point_size	numeric. Size of points. Default is 1.
point_alpha	numeric. Alpha value for points. Default is 0.9.
limits_expand	list. Expand the axis limits. Default is NULL.
limits_equal	logical. Set axis limits equal. Default is FALSE.
legend_title	logical. If FALSE, then the legend title is removed. Default is FALSE.
legend_position	character. Position of the legend. Default is "bottom". If NULL, then the legend's positioning is not jadjusted.
thm	ggplot2 theme. Specifies ggplot2 theme. Default is cowplot::theme_cowplot(), with a white plot background (as opposed to transparent).
grid	The value from calling cowplot::background_grid. Specifies display of grid lines. If NULL, then no background grid is displayed (recommended for non-cowplot-themed plots). Default is cowplot::background_grid(major = "xy"), which displays major grid lines on both x- and y-axes.
grp_to_col	character vector. Specifies colours for elements in grp. Elements are colours. If named, the names specify the level within grp to which the colours are matched. If NULL and only two groups are compared, then all points are black. If NULL and there are more than two groups compared, then defaults to palette Set1 of the RColorBrewer package. Default is NULL.
abline	logical. If TRUE, then the y=x line is plotted in colour "gray85". Default is TRUE.
smooth	logical. If TRUE, then a linear regression line is plotted.
smooth_method	character. Smoothing method to pass to geom_smooth. Default is "lm".
smooth_se	logical. Whether to display 95% confidence interval for the smooth line. Default is FALSE.

Examples

response_vec_a <- rnorm(5)
response_tbl <- data.frame(
  group = rep(letters[1:3], each = 5),
  response = c(
    response_vec_a,
    response_vec_a * 1.2 + rnorm(5, sd = 0.2),
    response_vec_a * 2 + rnorm(5, sd = 2)
  ),
  pid = rep(paste0("id_", 1:5), 3)
)
library(UtilsGGSV)
ggcorr(
  data = response_tbl,
  grp = "group",
  y = "response",
  id = "pid"
)

SATVILab/UtilsGGSV documentation built on Nov. 8, 2024, 8:41 p.m.