plot_marker_boxplot() generates faceted box plots of aggregated expression per sample grouped by a grouping of interest for each marker-cluster combination.
Usage
plot_marker_boxplot(
fcd,
marker = NULL,
expr_slot = "orig",
cluster_slot = "Phenograph_pca_orig_k_60",
cluster_var = "metaclusters",
cluster_to_show = NULL,
group_var,
sample_var,
fun = "median",
facet_by_clustering = F,
facet_ncol = 5,
color_palette = cluster_palette,
dot_size = 2
)Arguments
- fcd
flow cytometry data set, that has been subjected to clustering or cell type label prediction with cyCONDOR
- marker
marker in provided expr_slot that should be included in plotting. By default all features are 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
vector of characters indicating levels in cluster_var that should be included for plotting. By default all groups are plotted.
- group_var
string indicating variable name in cell_anno that should be used to group samples in sample_var
- sample_var
string indicating variable name in cell_anno that defines sample IDs to be used.
- fun
string indicating which aggregation of expression should be performed for each sample. Needs to be one out of "median" (default) or "mean".
- facet_by_clustering
logical indicating how to structure faceting of the plot. If set to FALSE (default) plot will be faceted by markers and clusters (or cell populations) are shown on x-axis. If set to TRUE, it is the other way around.
- facet_ncol
Number of columns to be used for faceting.
- color_palette
vector of colors that should be used to fill box plots.
- dot_size
numeric indicating the size of the dots.