vd_UMAP.RdGenerate UMAPs with each variance decomposition covariate overlaid.
vd_UMAP(object, vd_model.list)Seurat Object
Output from vd_Formula().
List ggplot handles, one for each model covariate.
parameter.list <- list(
covariates = c( "cluster", "percent.mt", "batch", "cycle", "seq.coverage"),
interactions = c("batch:cluster")
)
# step 1: model formulation
vd_model.list <- vd_Formula(object = so.query,
covariates = parameter.list$covariates,
interactions = parameter.list$interactions)
#> Error in vd_Formula(object = so.query, covariates = parameter.list$covariates, interactions = parameter.list$interactions): could not find function "vd_Formula"
# step 2: prep model inputs
vd_inputs.list <- vd_Inputs(object = so.query, vd_model.list = vd_model.list, features = NULL,
pct.min = 0.9, variable.features = F, subsample.factor = 1)
#> Error in vd_Inputs(object = so.query, vd_model.list = vd_model.list, features = NULL, pct.min = 0.9, variable.features = F, subsample.factor = 1): could not find function "vd_Inputs"
# step 3: run variance decomposition
vd_results.list <- vd_Run(vd_inputs.list, n.workers = 20)
#> Error in vd_Run(vd_inputs.list, n.workers = 20): could not find function "vd_Run"
# step 4 (optional): visualize UMAP distribution of covariates
plt.umap.list <- vd_UMAP(object = so.query, vd_model.list = vd_model.list)
#> Error in vd_UMAP(object = so.query, vd_model.list = vd_model.list): could not find function "vd_UMAP"
# step 5 (optional): visualize decomposition
res.var2 <- vd_results.list$varPart.format1
#> Error in eval(expr, envir, enclos): object 'vd_results.list' not found
plt.var <- plotVarPart( res.var2 ) +
theme_miko() +
labs(title = "Variance Decomposition", subtitle = "Linear Mixed-Effects Model") +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
#> Error in plotVarPart(res.var2): could not find function "plotVarPart"