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Merged
rcorces merged 1 commit into from
Jun 9, 2022
Merged

Dev guides #1466

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10 changes: 5 additions & 5 deletions R/ArchRBrowser.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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())
Expand Down Expand Up @@ -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{

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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,
Expand Down
6 changes: 3 additions & 3 deletions R/DoubletsScores.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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) +
Expand All @@ -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()) +
Expand All @@ -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) +
Expand Down
4 changes: 2 additions & 2 deletions R/Footprinting.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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))

Expand Down