DimPlotAtomic: Atomic Dimension Reduction Plot without splitting the data
In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

DimPlotAtomic

R Documentation

Atomic Dimension Reduction Plot without splitting the data

Description

Atomic Dimension Reduction Plot without splitting the data

Usage

DimPlotAtomic(
  data,
  dims = 1:2,
  group_by = NULL,
  group_by_sep = "_",
  features = NULL,
  lower_quantile = 0,
  upper_quantile = 0.99,
  lower_cutoff = NULL,
  upper_cutoff = NULL,
  pt_size = NULL,
  pt_alpha = 1,
  bg_color = "grey80",
  bg_cutoff = NULL,
  color_name = "",
  label_insitu = FALSE,
  show_stat = !identical(theme, "theme_blank"),
  label = FALSE,
  label_size = 4,
  label_fg = "white",
  label_bg = "black",
  label_bg_r = 0.1,
  label_repel = FALSE,
  label_repulsion = 20,
  label_pt_size = 1,
  label_pt_color = "black",
  label_segment_color = "black",
  highlight = NULL,
  highlight_alpha = 1,
  highlight_size = 1,
  highlight_color = "black",
  highlight_stroke = 0.8,
  add_mark = FALSE,
  mark_type = c("hull", "ellipse", "rect", "circle"),
  mark_expand = unit(3, "mm"),
  mark_alpha = 0.1,
  mark_linetype = 1,
  stat_by = NULL,
  stat_plot_type = c("pie", "ring", "bar", "line"),
  stat_plot_size = 0.1,
  stat_palette = "Set1",
  stat_args = list(),
  graph = NULL,
  edge_size = c(0.05, 0.5),
  edge_alpha = 0.1,
  edge_color = "grey40",
  add_density = FALSE,
  density_color = "grey80",
  density_filled = FALSE,
  density_filled_palette = "Greys",
  density_filled_palcolor = NULL,
  lineages = NULL,
  lineages_trim = c(0.01, 0.99),
  lineages_span = 0.75,
  lineages_palette = "Dark2",
  lineages_palcolor = NULL,
  lineages_arrow = ggplot2::arrow(length = unit(0.1, "inches")),
  lineages_linewidth = 1,
  lineages_line_bg = "white",
  lineages_line_bg_stroke = 0.5,
  lineages_whiskers = FALSE,
  lineages_whiskers_linewidth = 0.5,
  lineages_whiskers_alpha = 0.5,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  theme = "theme_this",
  theme_args = list(),
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  raster = NULL,
  raster_dpi = c(512, 512),
  hex = FALSE,
  hex_linewidth = 0.5,
  hex_count = !is.null(group_by),
  hex_bins = 50,
  hex_binwidth = NULL,
  palette = ifelse(is.null(features), "Paired", "Spectral"),
  palcolor = NULL,
  seed = 8525,
  ...
)

Arguments

`data`	A data frame.
`dims`	A character vector of the column names to plot on the x and y axes or a numeric vector of the column indices.
`group_by`	A character string of the column name to group the data. A character/factor column is expected. If multiple columns are provided, the columns will be concatenated with `group_by_sep`.
`group_by_sep`	A character string to concatenate the columns in `group_by`, if multiple columns are provided.
`features`	A character vector of the column names to plot as features.
`lower_quantile`, `upper_quantile`, `lower_cutoff`, `upper_cutoff`	Vector of minimum and maximum cutoff values or quantile values for each feature.
`pt_size`	A numeric value of the point size. If NULL, the point size will be calculated based on the number of data points.
`pt_alpha`	A numeric value of the point transparency. Default is 1.
`bg_color`	A character string of the background or NA points. Default is "grey80".
`bg_cutoff`	A numeric value to be used a cutoff to set the feature values to NA. Default is NULL.
`color_name`	A character string of the color legend name. Default is "".
`label_insitu`	Whether to place the raw labels (group names) in the center of the points with the corresponding group. Default is FALSE, which using numbers instead of raw labels.
`show_stat`	Whether to show the number of points in the subtitle. Default is TRUE.
`label`	Whether to show the labels of groups. Default is FALSE.
`label_size`	A numeric value of the label size. Default is 4.
`label_fg`	A character string of the label foreground color. Default is "white".
`label_bg`	A character string of the label background color. Default is "black".
`label_bg_r`	A numeric value of the background ratio of the labels. Default is 0.1.
`label_repel`	Whether to repel the labels. Default is FALSE.
`label_repulsion`	A numeric value of the label repulsion. Default is 20.
`label_pt_size`	A numeric value of the label point size. Default is 1.
`label_pt_color`	A character string of the label point color. Default is "black".
`label_segment_color`	A character string of the label segment color. Default is "black".
`highlight`	A character vector of the row names to highlight. Default is NULL.
`highlight_alpha`	A numeric value of the highlight transparency. Default is 1.
`highlight_size`	A numeric value of the highlight size. Default is 1.
`highlight_color`	A character string of the highlight color. Default is "black".
`highlight_stroke`	A numeric value of the highlight stroke. Default is 0.5.
`add_mark`	Whether to add mark to the plot. Default is FALSE.
`mark_type`	A character string of the mark type. Default is "hull".
`mark_expand`	A unit value of the mark expand. Default is 3mm.
`mark_alpha`	A numeric value of the mark transparency. Default is 0.1.
`mark_linetype`	A numeric value of the mark line type. Default is 1.
`stat_by`	A character string of the column name to calculate the statistics. Default is NULL.
`stat_plot_type`	A character string of the statistic plot type. Default is "pie".
`stat_plot_size`	A numeric value of the statistic plot size. Default is 0.1.
`stat_args`	A list of additional arguments to the statistic plot. Default is list(palette = "Set1").
`graph`	A character string of column names or the indexes in the data for the graph data. Default is NULL. If "@graph" is provided, the graph data will be extracted from the data attribute 'graph'.
`edge_size`	A numeric vector of the edge size range. Default is c(0.05, 0.5).
`edge_alpha`	A numeric value of the edge transparency. Default is 0.1.
`edge_color`	A character string of the edge color. Default is "grey40".
`add_density`	Whether to add density plot. Default is FALSE.
`density_color`	A character string of the density color. Default is "grey80".
`density_filled`	Whether to fill the density plot. Default is FALSE.
`density_filled_palette`	A character string of the filled density palette. Default is "Greys".
`density_filled_palcolor`	A character vector of the filled density palette colors. Default is NULL.
`lineages`	A character vector of the column names for lineages. Default is NULL.
`lineages_trim`	A numeric vector of the trim range for lineages. Default is c(0.01, 0.99).
`lineages_span`	A numeric value of the lineages span. Default is 0.75.
`lineages_palette`	A character string of the lineages palette. Default is "Dark2".
`lineages_palcolor`	A character vector of the lineages palette colors. Default is NULL.
`lineages_arrow`	An arrow object for the lineages. Default is arrow(length = unit(0.1, "inches")).
`lineages_linewidth`	A numeric value of the lineages line width. Default is 1.
`lineages_line_bg`	A character string of the lineages line background color. Default is "white".
`lineages_line_bg_stroke`	A numeric value of the lineages line background stroke. Default is 0.5.
`lineages_whiskers`	Whether to add whiskers to the lineages. Default is FALSE.
`lineages_whiskers_linewidth`	A numeric value of the lineages whiskers line width. Default is 0.5.
`lineages_whiskers_alpha`	A numeric value of the lineages whiskers transparency. Default is 0.5.
`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_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_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_byrow`	A logical value indicating whether to fill the plots by row. Default is TRUE.
`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.
`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.
`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.
`raster`	Whether to raster the plot. Default is NULL.
`raster_dpi`	A numeric vector of the raster dpi. Default is c(512, 512).
`hex`	Whether to use hex plot. Default is FALSE.
`hex_linewidth`	A numeric value of the hex line width. Default is 0.5.
`hex_count`	Whether to count the hex.
`hex_bins`	A numeric value of the hex bins. Default is 50.
`hex_binwidth`	A numeric value of the hex bin width. Default is NULL.
`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).
`seed`	The random seed to use. Default is 8525.
`...`	Additional arguments.