diff --git a/inst/rmarkdown/CeldaCG_PlotResults.Rmd b/inst/rmarkdown/CeldaCG_PlotResults.Rmd index 200a79e5..10e2bc45 100644 --- a/inst/rmarkdown/CeldaCG_PlotResults.Rmd +++ b/inst/rmarkdown/CeldaCG_PlotResults.Rmd @@ -199,42 +199,16 @@ for (i in seq_len(L)) { altExpName = altExpName, modules = i ) - # p2 <- moduleHeatmap( - # sce, - # featureModule = i, - # topCells = NULL, - # displayName = displayName, - # moduleLabel = "All cells", - # useRaster = TRUE - # ) - # p3 <- moduleHeatmap( - # sce, - # featureModule = i, - # topCells = 100, - # displayName = displayName, - # moduleLabel = "Top 100 cells", - # useRaster = TRUE - # ) - - fig <- multi_panel_figure(rows = 2, - columns = 2, - figure_name = paste0("fig", i)) - - fig <- fill_panel(fig, - p1, - row = 1, - column = 1:2, - label = "") - fig <- fill_panel(fig, - p2[[i]], - row = 2, - column = 1, - label = "") - fig <- fill_panel(fig, - p3[[i]], - row = 2, - column = 2, - label = "") + + plts <- list(p1,p2[[i]],p3[[i]]) + fig <- gridExtra::marrangeGrob(plts, + nrow = 2, + ncol = 2, + layout_matrix = matrix(c(1,1,2,3), + nrow = 2, + ncol = 2, + byrow = TRUE), + top = NA) fig.list[[i]] <- fig } for (i in seq_len(L)) { diff --git a/inst/rmarkdown/CeldaCG_Run.Rmd b/inst/rmarkdown/CeldaCG_Run.Rmd index 6c38912c..8f510de0 100644 --- a/inst/rmarkdown/CeldaCG_Run.Rmd +++ b/inst/rmarkdown/CeldaCG_Run.Rmd @@ -101,7 +101,7 @@ varFilter <- if (varFilter) { temp.sce <- sce temp.sce <- - seuratFindHVG(inSCE = temp.sce, useAssay = useAssay) + runSeuratFindHVG(inSCE = temp.sce, useAssay = useAssay) o <- head( order(