View source: R/auxiliary_giotto.R
filterCombinations | R Documentation |
Shows how many genes and cells are lost with combinations of thresholds.
filterCombinations(
gobject,
expression_values = c("raw", "normalized", "scaled", "custom"),
expression_thresholds = c(1, 2),
gene_det_in_min_cells = c(5, 50),
min_det_genes_per_cell = c(200, 400),
scale_x_axis = "identity",
x_axis_offset = 0,
scale_y_axis = "identity",
y_axis_offset = 0,
show_plot = TRUE,
return_plot = FALSE,
save_plot = NA,
save_param = list(),
default_save_name = "filterCombinations"
)
gobject |
giotto object |
expression_values |
expression values to use |
expression_thresholds |
all thresholds to consider a gene expressed |
gene_det_in_min_cells |
minimum number of cells that should express a gene to consider that gene further |
min_det_genes_per_cell |
minimum number of expressed genes per cell to consider that cell further |
scale_x_axis |
ggplot transformation for x-axis (e.g. log2) |
x_axis_offset |
x-axis offset to be used together with the scaling transformation |
scale_y_axis |
ggplot transformation for y-axis (e.g. log2) |
y_axis_offset |
y-axis offset to be used together with the scaling transformation |
show_plot |
show plot |
return_plot |
return only ggplot object |
save_plot |
directly save the plot [boolean] |
save_param |
list of saving parameters from |
default_save_name |
default save name for saving, don't change, change save_name in save_param |
Creates a scatterplot that visualizes the number of genes and cells that are lost with a specific combination of a gene and cell threshold given an arbitrary cutoff to call a gene expressed. This function can be used to make an informed decision at the filtering step with filterGiotto.
list of data.table and ggplot object
data(mini_giotto_single_cell)
# assess the effect of multiple filter criteria
filterCombinations(mini_giotto_single_cell,
gene_det_in_min_cells = c(2, 4, 8),
min_det_genes_per_cell = c(5, 10, 20))
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