FSV_sig {spatialDE} | R Documentation |
Plot Fraction Spatial Variance vs Q-value
FSV_sig( results, ms_results = NULL, certain_only = FALSE, log_x = FALSE, do_label = TRUE, covariate_names = NULL )
results |
results from SpatialDE. |
ms_results |
model selection results, should be a data frame with
columns |
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 |
covariate_names |
names of covariates as a reference, default to |
A ggplot2
object.
Davide Corso, Milan Malfait, Lambda Moses
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.
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)