View source: R/auxiliary_visuals.R
violinPlot | R Documentation |
Creates violinplot for selected clusters
violinPlot(
gobject,
spat_unit = NULL,
feat_type = NULL,
expression_values = c("normalized", "scaled", "custom"),
feats = NULL,
genes = NULL,
cluster_column,
cluster_custom_order = NULL,
color_violin = c("feats", "cluster"),
cluster_color_code = NULL,
strip_position = c("top", "right", "left", "bottom"),
strip_text = 7,
axis_text_x_size = 10,
axis_text_y_size = 6,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "violinPlot"
)
gobject |
giotto object |
spat_unit |
spatial unit (e.g. "cell") |
feat_type |
feature type (e.g. "rna", "dna", "protein") |
expression_values |
expression values to use (e.g. "normalized", "scaled", "custom") |
feats |
features to plot |
genes |
deprecated, use feats argument |
cluster_column |
name of column to use for clusters (e.g. "leiden_clus") |
cluster_custom_order |
custom order of clusters |
color_violin |
color violin according to "genes" or "clusters" |
cluster_color_code |
color code for clusters |
strip_position |
position of gene labels (e.g. "top", "right", "left", "bottom") |
strip_text |
size of strip text |
axis_text_x_size |
size of x-axis text |
axis_text_y_size |
size of y-axis text |
show_plot |
show plot. TRUE or FALSE |
return_plot |
return ggplot object. TRUE or FALSE |
save_plot |
directly save the plot. TRUE or FALSE |
save_param |
list of saving parameters, see |
default_save_name |
default save name for saving, don't change, change save_name in save_param |
ggplot
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