CorPlotAtomic: Atomic Correlation Plot
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

CorPlotAtomic

R Documentation

Atomic Correlation Plot

Description

Generate scatter correlation plot for two variables.

Usage

CorPlotAtomic(
  data,
  x,
  y,
  group_by = NULL,
  group_by_sep = "_",
  group_name = NULL,
  pt_size = 2,
  pt_shape = 16,
  alpha = 1,
  raster = FALSE,
  raster_dpi = c(512, 512),
  highlight = NULL,
  highlight_color = "black",
  highlight_size = 1,
  highlight_alpha = 1,
  highlight_stroke = 0.8,
  anno_items = c("eq", "r2", "p"),
  anno_size = 3,
  anno_fg = "black",
  anno_bg = "white",
  anno_bg_r = 0.1,
  anno_position = c("topleft", "topright", "bottomleft", "bottomright", "tl", "tr", "bl",
    "br"),
  add_smooth = TRUE,
  smooth_color = "red2",
  smooth_width = 1.5,
  smooth_se = FALSE,
  theme = "theme_this",
  theme_args = list(),
  palette = ifelse(is.null(group_by), "Spectral", "Paired"),
  palcolor = NULL,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  aspect.ratio = 1,
  legend.position = waiver(),
  legend.direction = "vertical",
  seed = 8525,
  ...
)

Arguments

`data`	A data frame.
`x`	y The column names of the data to be plotted.
`y`	A character string specifying the column name of the data frame to plot for the y-axis.
`group_by`	The column name of the data to be used for grouping. Different groups will be plotted in different colors.
`group_by_sep`	The separator used to concatenate multiple columns in `group_by`.
`group_name`	The name of the group in the legend.
`pt_size`	The size of the points.
`pt_shape`	The shape of the points.
`alpha`	A numeric value specifying the transparency of the plot.
`raster`	Whether to use raster graphics for plotting.
`raster_dpi`	The DPI of the raster graphics.
`highlight`	The items to be highlighted. Could be either a vector of rownames if data has rownames, or a vector of indices, or An expression that can be evaluated by `dplyr::filter` to get the highlighted items.
`highlight_color`	The color of the highlighted points.
`highlight_size`	The size of the highlighted points.
`highlight_alpha`	The alpha of the highlighted points.
`highlight_stroke`	The stroke of the highlighted points.
`anno_items`	The items to be annotated on the plot. Available items: "eq", "r2", "p", "spearman", "pearson", "kendall", "n".
`anno_size`	The size of the annotation text.
`anno_fg`	The color of the annotation text.
`anno_bg`	The background color of the annotation text.
`anno_bg_r`	The radius of the background of the annotation text.
`anno_position`	The position of the annotation text. Available positions: "topleft", "topright", "bottomleft", "bottomright". Shortcuts: "tl", "tr", "bl", "br".
`add_smooth`	Whether to add a linear regression line.
`smooth_color`	The color of the regression line.
`smooth_width`	The width of the regression line.
`smooth_se`	Whether to add the standard error band to the regression line.
`theme`	A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".
`theme_args`	A list of arguments to pass to the theme function.
`palette`	A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different `split_by` values.
`palcolor`	A character string specifying the color to use in the palette. A named list can be used to specify the colors for different `split_by` values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).
`title`	A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
`subtitle`	A character string specifying the subtitle of the plot.
`xlab`	A character string specifying the x-axis label.
`ylab`	A character string specifying the y-axis label.
`facet_by`	A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by `split_by` and generate multiple plots and combine them into one using `patchwork::wrap_plots`
`facet_scales`	Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See `ggplot2::facet_wrap`
`facet_ncol`	A numeric value specifying the number of columns in the facet. When facet_by is a single column and facet_wrap is used.
`facet_nrow`	A numeric value specifying the number of rows in the facet. When facet_by is a single column and facet_wrap is used.
`facet_byrow`	A logical value indicating whether to fill the plots by row. Default is TRUE.
`aspect.ratio`	A numeric value specifying the aspect ratio of the plot.
`legend.position`	A character string specifying the position of the legend. if `waiver()`, for single groups, the legend will be "none", otherwise "right".
`legend.direction`	A character string specifying the direction of the legend.
`seed`	The random seed to use. Default is 8525.
`...`	Additional arguments.