FSV_sig {spatialDE}R Documentation

Plot Fraction Spatial Variance vs Q-value

Description

Plot Fraction Spatial Variance vs Q-value

Usage

FSV_sig(
  results,
  ms_results = NULL,
  certain_only = FALSE,
  log_x = FALSE,
  do_label = TRUE,
  covariate_names = NULL
)

Arguments

results

results from SpatialDE.

ms_results

model selection results, should be a data frame with columns g for gene names and model for the model selected.

certain_only

only plot results with narrow 95% confidence interval.

log_x

Whether to display x axis in log scale.

do_label

display gene names for statistically significant genes, default TRUE.

covariate_names

names of covariates as a reference, default to NULL.

Value

A ggplot2 object.

Author(s)

Davide Corso, Milan Malfait, Lambda Moses

References

Svensson, V., Teichmann, S. & Stegle, O. SpatialDE: identification of spatially variable genes. Nat Methods 15, 343–346 (2018). https://doi.org/10.1038/nmeth.4636

SpatialDE 1.1.3: the version of the Python package used under the hood.

Examples

set.seed(42)
spe <- mockSVG(size = 10, tot_genes = 200, de_genes = 20, return_SPE = TRUE)
## Run spatialDE with S4 integration
results <- spatialDE(spe)
## Run model search
msearch <- modelSearch(spe, de_results = results, qval_thresh = NULL,
  verbose = FALSE)

plot <- FSV_sig(results, msearch)


[Package spatialDE version 0.99.10 Index]