density plot of marker expression in cell populations grouped by a meta variable
Source:R/data_visualization.R
plot_marker_density.Rd
plot_marker_density()
plots the density distribution of expression for cell populations. Each line indicates distribution for one level in group_var.
Usage
plot_marker_density(
fcd,
marker,
expr_slot = "orig",
cluster_slot,
cluster_var,
cluster_to_show = NULL,
group_var,
facet_var = NULL,
facet_ncol = 5,
color_palette = cluster_palette
)
Arguments
- fcd
flow cytometry data set, that has been subjected to clustering or cell type label prediction with cyCONDOR
- marker
vector of characters indicating which features of the expression matrix should be plotted.
- expr_slot
expr_slot from which to take marker expression values, default is "orig". Corrected input data should be handled cautiously.
- cluster_slot
string specifying which clustering slot to use to find variable specified in cluster_var
- cluster_var
string specifying variable name in cluster_slot that identifies cell population labels to be used (e.g. clusters, metaclusters or predicted labels).
- cluster_to_show
(optional) vector of strings indicating levels in cluster_var that should be included for plotting.
- group_var
string indicating variable name in cell_anno for which density distributions get calculated.
- facet_var
(optional) string indicating variable name in cell_anno that should be used to facet the plots by a meta variable.
- facet_ncol
numeric, number of columns used for faceting.
- color_palette
vector of colors to be used to color the density lines
Value
plot_marker_density()
returns either one plot in case only one marker is provided via marker
argument or a list of plots, if several markers are requested.
Details
plot_marker_density
The density plots are plotted with default parameters of ggplot2's geom_density
.