plot_dim_red() generates a dotplot of the coordinates of any dimensionality reduction performed on a condor object. The plot can be colored by any variable both numeric (e.g. expression) or categorical (e.g. clustering/metadata).
Usage
plot_dim_red(
fcd,
expr_slot = NULL,
reduction_method,
reduction_slot,
cluster_slot = NULL,
add_pseudotime = FALSE,
pseudotime_slot,
param,
order = FALSE,
title = "Dimensionality Reduction Plot",
limX = NULL,
limY = NULL,
dot_size = 0.1,
alpha = 0.2,
color_discrete = cluster_palette,
color_gradient = colors,
remove_guide = FALSE,
facet_by_variable = FALSE,
label_clusters = FALSE,
label_size = 3.5,
label_color = "black",
raster = FALSE,
seed = 91
)Arguments
- fcd
flow cytometry data set, that has been subjected to dimensionality reduction with cyCONDOR.
- expr_slot
expr_slot from which to take marker expression values, default is "orig". Corrected input data should be handled cautiously.
- reduction_method
string specifying which dimensionality reduction method to use ("umap", "tSNE", "diffmap", "pca").
- reduction_slot
string specifying reduction name in reduction_method to use for visualization, e.g. "pca_orig".
- cluster_slot
string specifying which clustering slot to use to find variable specified in cluster_var.
- add_pseudotime
Logical, if plot should be colored by pseudotime.
- pseudotime_slot
string specifying pseudotime name to use for visualization.
- param
parameter to visualize in the plot, this can be either a continuous variable or a categorical one, the function will react differently accordingly.
- order
logical if you want to order the dots in the plot, by expression for example. This can help to find small populations of positive cells. If set to FALSE, the plotting order of the cells is randomized.
- title
title of the plot.
- limX
limits of the x axes (e.g. c(-1, 7)).
- limY
limits of the y axes (e.g. c(-1, 7)).
- dot_size
size of the dots.
- alpha
transparency of the dots.
- color_discrete
colors for discrete parameters, must be provided as vector of the same length as the number of factors of `param`.
- color_gradient
colors for continuous parameters.
- remove_guide
logical, if you want to remove the guide.
- facet_by_variable
option to facet the plot by a variable, if FALSE the plot is not faceted, if TRUE the plot is faceted by the `param` variable. If any other variable is provided (e.g. "group") the plot will be faceted by this variable.
- label_clusters
logical: If clusters should be labeled with a text box.
- label_size
size of the labels.
- label_color
color of the labels.
- raster
TRUE or FALSE, if plot should be returned as raster image, this option lowers the quality of the plot but makes it easier to work with images with high number of cells.
- seed
seed is set for reproducibility.