From 5264d03c54e6e981f275f74696f299d3a03f8693 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 30 Jan 2018 14:41:38 +1100
Subject: [PATCH] Manually calculate RankCounts
---
R/compare.R | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/R/compare.R b/R/compare.R
index fb1f270..27ca039 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -306,6 +306,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
sce <- addFeatureStats(sce, "cpm", log = TRUE)
colData(sce)$PctZero <- 100 * (1 - colData(sce)$total_features /
nrow(sce))
+ rowData(sce)$RankCounts <- rank(rowData(sce)$mean_counts)
sces[[name]] <- sce
}
@@ -317,7 +318,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
ref.z.gene <- sort(rowData(ref.sce)$pct_dropout_counts)
ref.z.cell <- sort(colData(ref.sce)$PctZero)
- ref.rank.ord <- order(rowData(ref.sce)$rank_counts)
+ ref.rank.ord <- order(rowData(ref.sce)$RankCounts)
ref.vars.rank <- rowData(ref.sce)$VarLogCPM[ref.rank.ord]
ref.z.gene.rank <- rowData(ref.sce)$pct_dropout_counts[ref.rank.ord]
@@ -343,9 +344,9 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
colData(sce)$RefRankZeros
rowData(sce)$MeanRankVarDiff <- rowData(sce)$VarLogCPM -
- ref.vars.rank[rowData(sce)$rank_counts]
+ ref.vars.rank[rowData(sce)$RankCounts]
rowData(sce)$MeanRankZerosDiff <- rowData(sce)$pct_dropout_counts -
- ref.z.gene.rank[rowData(sce)$rank_counts]
+ ref.z.gene.rank[rowData(sce)$RankCounts]
sces[[name]] <- sce
}
@@ -391,7 +392,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
theme_minimal()
mean.var <- ggplot(features,
- aes_string(x = "rank_counts", y = "MeanRankVarDiff",
+ aes_string(x = "RankCounts", y = "MeanRankVarDiff",
colour = "Dataset", fill = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_point(size = point.size, alpha = point.alpha) +
@@ -434,7 +435,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
theme_minimal()
mean.zeros <- ggplot(features,
- aes_string(x = "rank_counts", y = "MeanRankZerosDiff",
+ aes_string(x = "RankCounts", y = "MeanRankZerosDiff",
colour = "Dataset", fill = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_point(size = point.size, alpha = point.alpha) +
--
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