diff --git a/vignettes/visium_cytassist_lungcancer.Rmd b/vignettes/visium_cytassist_lungcancer.Rmd index c84910261..3d72d19ee 100644 --- a/vignettes/visium_cytassist_lungcancer.Rmd +++ b/vignettes/visium_cytassist_lungcancer.Rmd @@ -330,9 +330,6 @@ signature_matrix = makeSignMatrixPAGE(sign_names = c('T_Cells', 'Macrophage', 'D pdcs_markers)) # 1.3 enrichment test with PAGE - -giotto_SC = getSpatialDataset(dataset = 'mol_cart_lung_873_C1', directory = data_path, method = "curl") - markers_scran = findMarkers_one_vs_all(gobject=giotto_SC, method="scran", expression_values="normalized", cluster_column = "leiden_clus", min_feats=3) @@ -479,7 +476,7 @@ heatmSpatialCorFeats(visium_lungcancer, heatmap_legend_param = list(title = NULL)) ``` -![](images/visium_cytassist_lungcancer/22-z1-heatmap_correlated_genes.pdf){width="50.0%"} +![](images/visium_cytassist_lungcancer/22-z1-heatmap_correlated_genes.png){width="50.0%"} ```{r, eval=FALSE} # 4. rank spatial correlated clusters and show genes for selected clusters