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1.5.0
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Khodadadi-Jamayran authored and Khodadadi-Jamayran committed May 7, 2020
1 parent 0f5d66a commit f00d467
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ RoxygenNote: 7.0.2
BugReports: https://github.com/rezakj/iCellR/issues
URL: https://github.com/rezakj/iCellR
NeedsCompilation: no
Packaged: 2020-05-07 15:52:00 UTC; khodaa01
Packaged: 2020-05-07 16:11:55 UTC; khodaa01
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),
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18 changes: 9 additions & 9 deletions R/F005.stats.plot.R
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Expand Up @@ -64,44 +64,44 @@ if (do == 2) {
geom_violin(trim=FALSE, col = "black", alpha = cell.transparency) +
geom_boxplot( fill = box.color, col = "green", notch = FALSE, outlier.shape = NA, alpha = cell.transparency) +
xlab("mito.percent") + ylab("percent of mito genes per cell") +
stat_summary(fun.y=mean, geom="point", size=2, color="black") +
stat_summary(fun=mean, geom="point", size=2, color="black") +
theme_bw() + theme(axis.text.x=element_text(angle=90))
# nGenes
nGenes.plot <- ggplot(DATA,aes(y=nGenes,x=col.legend)) +
geom_jitter(color = cell.color, size = cell.size, alpha = cell.transparency) +
geom_violin(trim=FALSE, col = "black", alpha = cell.transparency) +
geom_boxplot( fill = box.color, col = box.line.col, notch = FALSE, outlier.shape = NA, alpha = cell.transparency) +
xlab("nGenes") + ylab("number of genes per cell") +
stat_summary(fun.y=mean, geom="point", size=2, color="black") +
stat_summary(fun=mean, geom="point", size=2, color="black") +
theme_bw() + theme(axis.text.x=element_text(angle=90))
# UMIs
UMIsplot <- ggplot(DATA,aes(y=UMIs,x=col.legend)) +
geom_jitter(color = cell.color, size = cell.size, alpha = cell.transparency) +
geom_violin(trim=FALSE, col = "black", alpha = cell.transparency) +
geom_boxplot( fill = box.color, col = box.line.col, notch = FALSE, outlier.shape = NA, alpha = cell.transparency) +
xlab("UMIs") + ylab("number of UMIs per cell") +
stat_summary(fun.y=mean, geom="point", size=2, color="black") +
stat_summary(fun=mean, geom="point", size=2, color="black") +
theme_bw() + theme(axis.text.x=element_text(angle=90))
# s.phase
s.plot <- ggplot(DATA,aes(y=S.phase.probability,x=col.legend)) +
geom_jitter(color = cell.color, size = cell.size, alpha = cell.transparency) +
geom_violin(trim=FALSE, col = "black", alpha = cell.transparency) +
geom_boxplot( fill = box.color, col = box.line.col, notch = FALSE, outlier.shape = NA, alpha = cell.transparency) +
xlab("S phase") + ylab("S phase probability") +
stat_summary(fun.y=mean, geom="point", size=2, color="black") +
stat_summary(fun=mean, geom="point", size=2, color="black") +
theme_bw() + theme(axis.text.x=element_text(angle=90))
# g2m.phase.probability
g2m.plot <- ggplot(DATA,aes(y=g2m.phase.probability,x=col.legend)) +
geom_jitter(color = cell.color, size = cell.size, alpha = cell.transparency) +
geom_violin(trim=FALSE, col = "black", alpha = cell.transparency) +
geom_boxplot( fill = box.color, col = box.line.col, notch = FALSE, outlier.shape = NA, alpha = cell.transparency) +
xlab("G2 and M phase") + ylab("G2 and M phase probability") +
stat_summary(fun.y=mean, geom="point", size=2, color="black") +
stat_summary(fun=mean, geom="point", size=2, color="black") +
theme_bw() + theme(axis.text.x=element_text(angle=90))
# scatter plots
if (col.legend[1] == ".") {
Mito.UMIs <- ggplot(DATA,aes(y=mito.percent,x=UMIs,
text = paste("UMIs =",DATA$UMIs,",",DATA$CellIds,sep=" "))) +
text = paste("UMIs =",UMIs,",",CellIds,sep=" "))) +
geom_point(color = cell.color, size = cell.size, alpha = cell.transparency) +
scale_x_continuous(trans = "log1p") +
scale_color_discrete(name="") +
Expand All @@ -110,7 +110,7 @@ if (do == 2) {
legend.key = element_rect(fill = back.col)) + theme_bw()
#
Genes.UMIs <- ggplot(DATA,aes(y=nGenes,x=UMIs,
text = paste("nGenes =",DATA$nGenes,",",DATA$CellIds,sep=" "))) +
text = paste("nGenes =",nGenes,",",CellIds,sep=" "))) +
geom_point(color = cell.color, size = cell.size, alpha = cell.transparency) +
scale_x_continuous(trans = "log1p") +
scale_y_continuous(trans = "log1p") +
Expand All @@ -120,7 +120,7 @@ if (do == 2) {
legend.key = element_rect(fill = back.col)) + theme_bw()
} else {
Mito.UMIs <- ggplot(DATA,aes(y=mito.percent,x=UMIs, col = col.legend,
text = paste("UMIs =",DATA$UMIs,",",DATA$CellIds,sep=" "))) +
text = paste("UMIs =",UMIs,",",CellIds,sep=" "))) +
geom_point( size = cell.size, alpha = cell.transparency) +
scale_x_continuous(trans = "log1p") +
scale_color_discrete(name="") +
Expand All @@ -129,7 +129,7 @@ if (do == 2) {
legend.key = element_rect(fill = back.col)) + theme_bw()
#
Genes.UMIs <- ggplot(DATA,aes(y=nGenes,x=UMIs, col = col.legend,
text = paste("nGenes =",DATA$nGenes,",",DATA$CellIds,sep=" "))) +
text = paste("nGenes =",nGenes,",",CellIds,sep=" "))) +
geom_point(size = cell.size, alpha = cell.transparency) +
scale_x_continuous(trans = "log1p") +
scale_y_continuous(trans = "log1p") +
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