Visualize data in dimensional reduction coordinates

Visualize proportions or expression in dimensional reduction coordinates.

plot_dimensional_reduction(
  dturtle,
  reduction_df,
  genes = NULL,
  plot = "proportions",
  include_gene = TRUE,
  log_expression = TRUE,
  include_labels = TRUE,
  reduction_to_use = "umap",
  indicate_significant_tx = TRUE,
  plot_colors = c("grey", "#9ECAE1", "#6BAED6", "#4292C6", "#2171B5", "#08519C",
    "#08306B"),
  plot_scale = "fixed",
  point_alpha = 1,
  point_size = NULL,
  text_size = 11,
  label_size = 3,
  label_colors = c("#7CAE00", "#00BFC4"),
  label_y_expansion = 0.2,
  savepath = NULL,
  filename_ext = "_dim_reduce.png",
  add_to_table = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

Arguments

dturtle	`dturtle` result object of `posthoc_and_stager()`.
reduction_df	Provide the reduction coordinates for each cell, either as a two column data frame or matrix (with cell identifiers as row names) or a Seurat object. If a Seurat object is provided, the reduction `reduction_to_use` will be pulled from the object.
genes	Character vector of genes to plot. If `NULL`, defaults to all found significant genes (`sig_genes`).
plot	Specify what values should be plotted. Can be `'proportions'` or `'expression'`.
include_gene	If `plot='expression'`, define if summarized gene expression should be plotted alongside.
log_expression	If `plot='expression'`, define if expression counts should be log transformed.
include_labels	Specify if labels of mean fitted proportional difference shall be included. The numbers in the labels are in regard to comparison group2 vs group1, in contrast to the dtu table.
reduction_to_use	Only relevant if a Seurat object is provided to `reduction_df`. Specify the name of the reduction to use in the object.
indicate_significant_tx	Specify if significant transcripts should be indicated in the plot by a colored strip. Converts the resulting plots to `grob`.
plot_colors	Specify a vector of minimum 2 colors that build the color scale.
plot_scale	Specify how the scales of each facet should act. Values are "fixed", "free_x", "free_y" or "free", to either have the same fixed scale, a free x- or y-axis or both axis free.
point_alpha	Specify an alpha level for the single cells / samples.
point_size	Specify the size of the points representing a single cell / sample. If `NULL`, chosen automatically.
text_size	Specify basic text size (in pt) to use in plot.
label_size	If `include_labels=TRUE`, set size of labels (in mm).
label_colors	If `include_labels=TRUE`, set color of labels of positive or negative proportional differences.
label_y_expansion	If `include_labels=TRUE`, define the factor the y-axis is extended by. This extension is performed to avoid overlapping of labels and cells / samples. Labels are added to bottom of the plots of the second comparison group.
savepath	If you want your files to be saved to disk, specify a save path here. The directories will be created if necessary.
filename_ext	Optionally specify a file name extension here, which also defines the save image format. The file name will be 'gene_name+extension'.
add_to_table	If a `savepath` is provided, add the filepaths of the created plots to the corresponding entries in `dtu_table`. The name of the column that shall be created can be specified here.
BPPARAM	If multicore processing should be used, specify a `BiocParallelParam` object here. Among others, can be `SerialParam()` (default) for non-multicore processing or `MulticoreParam('number_cores')` for multicore processing. See `BiocParallel` for more information.
...	Arguments passed on to `ggplot2::ggsave` `filename` File name to create on disk. `device` Device to use. Can either be a device function (e.g. `png()`), or one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only). `path` Path of the directory to save plot to: `path` and `filename` are combined to create the fully qualified file name. Defaults to the working directory. `scale` Multiplicative scaling factor. `width` Plot size in `units` ("in", "cm", or "mm"). If not supplied, uses the size of current graphics device. `height` Plot size in `units` ("in", "cm", or "mm"). If not supplied, uses the size of current graphics device. `units` Plot size in `units` ("in", "cm", or "mm"). If not supplied, uses the size of current graphics device. `dpi` Plot resolution. Also accepts a string input: "retina" (320), "print" (300), or "screen" (72). Applies only to raster output types. `limitsize` When `TRUE` (the default), `ggsave` will not save images larger than 50x50 inches, to prevent the common error of specifying dimensions in pixels.

Value

Returns list of saved plots, for adding to the DTU table. If no savepath is provided, returns a list of the created plots for further processing. If indicate_significant_tx is TRUE, a list of grob objects will be returned, otherwise a list of ggplot objects. grob can be visualized for example with grid::grid.draw().

Details

Needs a pre-computed dimensional reduction with at least 2 dimensions. Currently only able to visualize in 2D. Sorts values to show highest expressing cells/samples on top.

Arguments

Value

Details

See also