diff --git a/R/ArchRBrowser.R b/R/ArchRBrowser.R index 1e76ddc7..41df3315 100644 --- a/R/ArchRBrowser.R +++ b/R/ArchRBrowser.R @@ -1044,7 +1044,7 @@ plotBrowserTrack <- function( margin = margin(0,0.35,0,0.35, "cm")), strip.text.y = element_text(angle = 0), strip.background = element_rect(color="black")) + - guides(fill = FALSE, colour = FALSE) + ggtitle(title) + guides(fill = "none", colour = "none") + ggtitle(title) p @@ -1346,7 +1346,7 @@ plotBrowserTrack <- function( theme(axis.title.x=element_blank(), axis.text.x=element_blank(),axis.ticks.x=element_blank()) + theme(axis.title.y=element_blank(), axis.text.y=element_blank(),axis.ticks.y=element_blank()) + theme(legend.text = element_text(size = baseSize), strip.text.y = element_text(size = facetbaseSize, angle = 0)) + - guides(fill = guide_legend(override.aes = list(colour = NA, shape = "c", size=3)), color = FALSE) + + guides(fill = guide_legend(override.aes = list(colour = NA, shape = "c", size=3)), color = "none") + theme(legend.position="bottom") + theme(legend.title=element_text(size=5), legend.text=element_text(size=7), legend.key.size = unit(0.75,"line"), legend.background = element_rect(color =NA), strip.background = element_blank()) @@ -1475,7 +1475,7 @@ plotBrowserTrack <- function( scale_color_manual(values = pal) + theme(legend.text = element_text(size = baseSize)) + theme_ArchR(baseSize = baseSize, baseLineSize = borderWidth, baseRectSize = borderWidth) + - guides(color = FALSE, fill = FALSE) + theme(strip.text.y = element_text(size = facetbaseSize, angle = 0), strip.background = element_blank()) + guides(color = "none", fill = "none") + theme(strip.text.y = element_text(size = facetbaseSize, angle = 0), strip.background = element_blank()) }else{ @@ -1795,7 +1795,7 @@ plotBrowserTrack <- function( margin = margin(0,0.35,0,0.35, "cm")), strip.text.y = element_text(angle = 0), strip.background = element_rect(color="black")) + - guides(fill = FALSE, colour = FALSE) + ggtitle(title) + guides(fill = "none", colour = "none") + ggtitle(title) p @@ -1884,7 +1884,7 @@ plotBrowserTrack <- function( pal = pal ) + facet_wrap(x~., ncol=1,scales="free_y",strip.position="right") + - guides(fill = FALSE, colour = FALSE) + + guides(fill = "none", colour = "none") + theme_ArchR(baseSize = baseSize, baseRectSize = borderWidth, baseLineSize = tickWidth, diff --git a/R/DoubletsScores.R b/R/DoubletsScores.R index c5338195..9275bd5f 100644 --- a/R/DoubletsScores.R +++ b/R/DoubletsScores.R @@ -378,7 +378,7 @@ addDoubletScores <- function( scale_colour_gradientn(colors = pal) + xlab("UMAP Dimension 1") + ylab("UMAP Dimension 2") + labs(color = "Simulated Doublet Density") + - guides(fill = FALSE) + theme_ArchR(baseSize = 10) + + guides(fill = "none") + theme_ArchR(baseSize = 10) + theme(axis.text.x = element_blank(), axis.ticks.x = element_blank(), axis.text.y = element_blank(), axis.ticks.y = element_blank()) + coord_equal(ratio = diff(xlim)/diff(ylim), xlim = xlim, ylim = ylim, expand = FALSE) + @@ -395,7 +395,7 @@ addDoubletScores <- function( # geom_point(data = dfDoub, aes(x=x,y=y,colour=color), size = 0.5) + # scale_colour_gradientn(colors = pal) + # xlab("UMAP Dimension 1") + ylab("UMAP Dimension 2") + - # guides(fill = FALSE) + theme_ArchR(baseSize = 10) + + # guides(fill = "none") + theme_ArchR(baseSize = 10) + # labs(color = "Simulated Doublet Density") + # theme(axis.text.x = element_blank(), axis.ticks.x = element_blank(), # axis.text.y = element_blank(), axis.ticks.y = element_blank()) + @@ -413,7 +413,7 @@ addDoubletScores <- function( # scale_colour_gradientn(colors = pal) + # xlab("UMAP Dimension 1") + ylab("UMAP Dimension 2") + # labs(color = "Simulated Doublet Density") + - # guides(fill = FALSE) + theme_ArchR(baseSize = 10) + + # guides(fill = "none") + theme_ArchR(baseSize = 10) + # theme(axis.text.x = element_blank(), axis.ticks.x = element_blank(), # axis.text.y = element_blank(), axis.ticks.y = element_blank()) + # coord_equal(ratio = diff(xlim)/diff(ylim), xlim = xlim, ylim = ylim, expand = FALSE) + diff --git a/R/Footprinting.R b/R/Footprinting.R index 5fd214da..9447cdd3 100644 --- a/R/Footprinting.R +++ b/R/Footprinting.R @@ -578,8 +578,8 @@ plotFootprints <- function( ylim = c(quantile(plotFootDF$mean, 0.0001), 1.15*quantile(smoothFoot, 0.999)), xlim = c(min(plotFootDF$x),max(plotFootDF$x)) ) + theme_ArchR(baseSize = baseSize) + ggtitle(name) + - guides(fill = FALSE) + - guides(color = FALSE) + ylab(paste0(title,"Normalized Insertions")) + guides(fill = "none") + + guides(color = "none") + ylab(paste0(title,"Normalized Insertions")) #removed ggrepel due to incompatibility with coord_cartesian - see https://github.com/GreenleafLab/ArchR/issues/493#issuecomment-870012873 #ggrepel::geom_label_repel(data = plotMax, aes(label = group), size = 3, xlim = c(75, NA))