Plot reduced dimensions (PCA, TSNE, UMAP)

Source: R/plotting_functions.R

Plot reduced dimensions (PCA, TSNE, UMAP)

plot_reduced_dim_scExp(
  scExp,
  color_by = "sample_id",
  reduced_dim = c("PCA", "TSNE", "UMAP"),
  select_x = NULL,
  select_y = NULL,
  downsample = 5000,
  transparency = 0.6,
  size = 1,
  max_distanceToTSS = 1000,
  annotate_clusters = "cell_cluster" %in% colnames(colData(scExp)),
  min_quantile = 0.01,
  max_quantile = 0.99
)

Arguments

scExp

A SingleCellExperiment Object
color_by

Character of eature used for coloration. Can be cell metadata ('total_counts', 'sample_id', ...) or a gene name.
reduced_dim

Reduced Dimension used for plotting
select_x

Which variable to select for x axis
select_y

Which variable to select for y axis
downsample

Number of cells to downsample
transparency

Alpha parameter, between 0 and 1
size

Size of the points.
max_distanceToTSS

The maximum distance to TSS to consider a gene linked to a region. Used only if "color_by" is a gene name.
annotate_clusters

A logical indicating if clusters should be labelled. The 'cell_cluster' column should be present in metadata.
min_quantile

The lower threshold to remove outlier cells, as quantile of cell embeddings (between 0 and 0.5).
max_quantile

The upper threshold to remove outlier cells, as quantile of cell embeddings (between 0.5 and 1).

Value

A ggplot geom_point plot of reduced dimension 2D reprensentation

Examples

data("scExp")
plot_reduced_dim_scExp(scExp, color_by = "sample_id")

plot_reduced_dim_scExp(scExp, color_by = "total_counts")

plot_reduced_dim_scExp(scExp, reduced_dim = "UMAP")

plot_reduced_dim_scExp(scExp, color_by = "CD52",  reduced_dim = "UMAP")