filterDistributions

Show feature or cell distribution after filtering on expression threshold. General sum and mean statistics for the expression values can also be plotted, however these are not affected by the expression_threshold value.

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"),
  nr_bins = 30,
  fill_color = "lightblue",
  scale_y = "identity",
  scale_axis = "identity",
  axis_offset = 0,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "filterDistributions"
)

Arguments

gobject

giotto object

feat_type

feature type (e.g. "rna", "dna", "protein")

spat_unit

spatial unit (e.g. "cell")

expression_values

character. Name of set of expression values to use. (default = "raw")

method

character. One of "threshold" (default), "sum", "mean". Method to create distribution (see details)

expression_threshold

numeric (default = 1). Threshold to consider a feature expressed. Applied only for method = "threshold"

detection

character. One of "feats" (default) or "cells". Calculate statistics based on features (e.g. genes) or cells/observations

plot_type

character. One of "histogram" (default) or "violin". Type of plot to create.

nr_bins

numeric. Number of bins for histogram plot

fill_color

fill color for plots. (Default = "lightblue")

scale_y

character. Scaling operation to apply on y-axis (e.g. "log")

scale_axis

character. ggplot2 transformation for axis (e.g. "log2"). This is passed to the transform param of ggplot2::scale_x_continuous()

axis_offset

numeric. offset to be used together with the scaling transformation

show_plot

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

save_param

list of saving parameters, see showSaveParameters

default_save_name

default save name for saving, don't change, change save_name in save_param

Value

ggplot object

Details

The distribution to plot is calculated based on the detection and method params. detection decides if values are computed rowwise ("feats") or colwise ("cells") across the feature x cell expression matrix. method determines how the distribution is calculated:

• "threshold" - calculate number of features that cross the expression_threshold (default)

• "sum" - find the sum of the features, i.e. total of a feature across all observations.

• "mean" - find the mean of the features, i.e. average expression

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.12

# visualize feature expression prevalence across observations (histogram)
filterDistributions(g)

# visualize with a threshold of 3
filterDistributions(g, expression_threshold = 3)

# visualize sum of feature expression across dataset
filterDistributions(g, method = "sum")

# visualize with a log scaling
filterDistributions(g, method = "sum", scale_axis = "log2")


# visualize as violinplot
filterDistributions(g, plot_type = "violin")

# visualize mean expression per cell
filterDistributions(g,
    detection = "cell",
    plot_type = "violin",
    method = "mean",
    scale_axis = "log2"
)