filterDistributions#
Last Updated: Oct 02, 2023
Description#
show gene or cell distribution after filtering on expression threshold
Usage#
filterDistributions(
gobject,
feat_type = NULL,
spat_unit = NULL,
expression_values = c("raw", "normalized", "scaled", "custom"),
method = c("threshold", "sum", "mean"),
expression_threshold = 1,
detection = c("feats", "cells"),
plot_type = c("histogram", "violin"),
scale_y = NULL,
nr_bins = 30,
fill_color = "lightblue",
scale_axis = "identity",
axis_offset = 0,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "filterDistributions"
)
Arguments#
|
giotto object |
|
feature type |
|
spatial unit |
|
expression values to use |
|
method to create distribution (see details) |
|
threshold to consider a gene expressed |
|
consider features (e.g. genes) or cells |
|
type of plot |
|
scale y-axis (e.g. “log”), NULL = no scaling |
|
number of bins for histogram plot |
|
fill color for plots |
|
ggplot transformation for axis (e.g. log2) |
|
offset to be used together with the scaling transformation |
|
show plot |
|
return ggplot object |
|
directly save the plot [boolean] |
|
list of saving parameters from
|
|
default save name for saving, don’t change, change save_name in save_param |
|
There are 3 ways to create a
distribution profile and
summarize it for either the
features or the cells (spatial
units)
|
Value#
ggplot object