do_GeyserPlot: Generate a Geyser plot.

In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Generate a Geyser plot.

Description

A Geyser plot is a custom plot in which we plot continuous values on the Y axis grouped by a categorical value in the X. This is plotted as a dot plot, jittered so that the dots span all the way to the other groups. On top of this, the mean and .66 and .95 of the data is plotted, depicting the overall distribution of the dots. The cells can, then, be colored by a continuous variable (same as Y axis or different) or a categorical one (same as X axis or different).

Usage

do_GeyserPlot(
  sample,
  features,
  assay = NULL,
  slot = "data",
  group.by = NULL,
  split.by = NULL,
  enforce_symmetry = FALSE,
  scale_type = "continuous",
  order = TRUE,
  plot_cell_borders = TRUE,
  jitter = 0.45,
  pt.size = 1,
  border.size = 2,
  border.color = "black",
  legend.position = "bottom",
  legend.width = 1,
  legend.length = 20,
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  legend.type = "colorbar",
  font.size = 14,
  font.type = "sans",
  axis.text.x.angle = 45,
  viridis.palette = "G",
  viridis.direction = 1,
  colors.use = NULL,
  na.value = "grey75",
  legend.ncol = NULL,
  legend.nrow = NULL,
  legend.icon.size = 4,
  legend.byrow = FALSE,
  legend.title = NULL,
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  xlab = "Groups",
  ylab = feature,
  flip = FALSE,
  min.cutoff = rep(NA, length(features)),
  max.cutoff = rep(NA, length(features)),
  number.breaks = 5,
  diverging.palette = "RdBu",
  diverging.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = -1,
  use_viridis = TRUE,
  plot.title.face = "bold",
  plot.subtitle.face = "plain",
  plot.caption.face = "italic",
  axis.title.face = "bold",
  axis.text.face = "plain",
  legend.title.face = "bold",
  legend.text.face = "plain"
)

Arguments

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
features	character | Features to represent.
assay	character | Assay to use. Defaults to the current assay.
slot	character | Data slot to use. Only one of: counts, data, scale.data. Defaults to "data".
group.by	character | Metadata variable to group the output by. Has to be a character of factor column.
split.by	character | Secondary metadata variable to further group (split) the output by. Has to be a character of factor column.
enforce_symmetry	logical | Return a symmetrical plot axes-wise or continuous color scale-wise, when applicable.
scale_type	character | Type of color scale to use. One of: categorical: Use a categorical color scale based on the values of "group.by". continuous: Use a continuous color scale based on the values of "feature".
order	logical | Whether to order the groups by the median of the data (highest to lowest).
plot_cell_borders	logical | Whether to plot border around cells.
jitter	numeric | Amount of jitter in the plot along the X axis. The lower the value, the more compacted the dots are.
pt.size	numeric | Size of the dots.
border.size	numeric | Width of the border of the cells.
border.color	character | Color for the border of the heatmap body.
legend.position	character | Position of the legend in the plot. One of: top: Top of the figure. bottom: Bottom of the figure. left: Left of the figure. right: Right of the figure. none: No legend is displayed.
legend.length, legend.width	numeric | Length and width of the legend. Will adjust automatically depending on legend side.
legend.framewidth, legend.tickwidth	numeric | Width of the lines of the box in the legend.
legend.framecolor	character | Color of the lines of the box in the legend.
legend.tickcolor	character | Color of the ticks of the box in the legend.
legend.type	character | Type of legend to display. One of: normal: Default legend displayed by ggplot2. colorbar: Redefined colorbar legend, using guide_colorbar.
font.size	numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.
font.type	character | Base font family for the plot. One of: mono: Mono spaced font. serif: Serif font family. sans: Default font family.
axis.text.x.angle	numeric | Degree to rotate the X labels. One of: 0, 45, 90.
viridis.palette	character | A capital letter from A to H or the scale name as in scale_fill_viridis.
viridis.direction	numeric | Either 1 or -1. Controls how the gradient of viridis scale is formed.
colors.use	character | Named vector of colors to use. Has to match the unique values of group.by when scale_type is set to categorical.
na.value	character | Color value for NA.
legend.ncol	numeric | Number of columns in the legend.
legend.nrow	numeric | Number of rows in the legend.
legend.icon.size	numeric | Size of the icons in legend.
legend.byrow	logical | Whether the legend is filled by row or not.
legend.title	character | Title for the legend.
plot.title, plot.subtitle, plot.caption	character | Title, subtitle or caption to use in the plot.
xlab, ylab	character | Titles for the X and Y axis.
flip	logical | Whether to invert the axis of the displayed plot.
min.cutoff, max.cutoff	numeric | Set the min/max ends of the color scale. Any cell/group with a value lower than min.cutoff will turn into min.cutoff and any cell with a value higher than max.cutoff will turn into max.cutoff. In FeaturePlots, provide as many values as features. Use NAs to skip a feature.
number.breaks	numeric | Controls the number of breaks in continuous color scales of ggplot2-based plots.
diverging.palette	character | Type of symmetrical color palette to use. Out of the diverging palettes defined in brewer.pal.
diverging.direction	numeric | Either 1 or -1. Direction of the divering palette. This basically flips the two ends.
sequential.palette	character | Type of sequential color palette to use. Out of the sequential palettes defined in brewer.pal.
sequential.direction	numeric | Direction of the sequential color scale. Either 1 or -1.
use_viridis	logical | Whether to use viridis color scales.
plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face	character | Controls the style of the font for the corresponding theme element. One of: plain: For normal text. italic: For text in itallic. bold: For text in bold. bold.italic: For text both in itallic and bold.

Details

Special thanks to Christina Blume for coming up with the name of the plot.

Value

Either a plot of a list of plots, depending on the number of features provided.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_GeyserPlot", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds", package = "SCpubr"))

    # Geyser plot with categorical color scale.
    p <- SCpubr::do_GeyserPlot(sample = sample,
                              features = "nCount_RNA",
                              scale_type = "categorical")
    p

    # Geyser plot with continuous color scale.
    p <- SCpubr::do_GeyserPlot(sample = sample,
                              features = "nCount_RNA",
                              scale_type = "continuous")


    p

  } else if (base::isFALSE(value)){
    message("This function can not be used without its suggested packages.")
    message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
  }

enblacar/SCpubr documentation built on Aug. 25, 2024, 9:45 p.m.