plot_marker_dotplot() generates a classical scatter plot of two markers
Usage
plot_marker_dotplot(
fcd,
expr_slot = "orig",
marker_x,
marker_y,
cluster_slot,
cluster_var,
cluster_to_show = NULL,
group_var = NULL,
order = F,
seed = 91,
color_palette = cluster_palette,
dot_size = 2,
title = ""
)Arguments
- fcd
flow cytometry data set, that has been subjected to clustering or cell type label prediction with cyCONDOR
- expr_slot
expr_slot from which to take marker expression values, default is "orig". Corrected input data should be handled cautiously.
- marker_x
marker name in expr slot of which transformed expression is shown on x-axis.
- marker_y
marker name in expr slot of which transformed expression is shown on y-axis.
- 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 characters indicating levels in cluster_var that should be included for plotting. By default all groups are plotted.
- group_var
(optional) string indicating variable name in cell_anno that should be used to color dots in plot. If not used, dots are clustered by cluster_var.
- order
logical if you want to order the dots in the plot by the variable used for coloring (TRUE). If set to FALSE (default), order of the cells is randomized.
- seed
a seed is set for reproducibility of the plotting result.
- color_palette
vector of colors that should be used to color dots.
- dot_size
numeric indicating the size of the dots.
- title
Title of the plot.
Value
The function returns a scatter plot of two features available in the expression matrix. By default, dots are colored by cell population label provided in cluster_var. If coloring by a metadata is wanted instead, a group_var can be defined. Further, if only a selection of levels available in cluster_var should be included in plotting, a vector of labels of interest can be provided to cluster_to_show argument.