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## ----eval=TRUE, warning=FALSE, message=FALSE----------------------------------
# Load required packages
library(alakazam)
library(dplyr)
library(scales)
# Subset example data
data(ExampleDb)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Quantify usage at the gene level
gene <- countGenes(ExampleDb, gene="v_call", groups="sample_id", mode="gene")
head(gene, n=4)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Assign sorted levels and subset to IGHV1
ighv1 <- gene %>%
mutate(gene=factor(gene, levels=sortGenes(unique(gene), method="name"))) %>%
filter(getFamily(gene) == "IGHV1")
# Plot V gene usage in the IGHV1 family by sample
g1 <- ggplot(ighv1, aes(x=gene, y=seq_freq)) +
theme_bw() +
ggtitle("IGHV1 Usage") +
theme(axis.text.x=element_text(angle=45, hjust=1, vjust=1)) +
ylab("Percent of repertoire") +
xlab("") +
scale_y_continuous(labels=percent) +
scale_color_brewer(palette="Set1") +
geom_point(aes(color=sample_id), size=5, alpha=0.8)
plot(g1)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Quantify V family usage by sample
family <- countGenes(ExampleDb, gene="v_call", groups="sample_id", mode="family")
# Plot V family usage by sample
g2 <- ggplot(family, aes(x=gene, y=seq_freq)) +
theme_bw() +
ggtitle("Family Usage") +
theme(axis.text.x=element_text(angle=45, hjust=1, vjust=1)) +
ylab("Percent of repertoire") +
xlab("") +
scale_y_continuous(labels=percent) +
scale_color_brewer(palette="Set1") +
geom_point(aes(color=sample_id), size=5, alpha=0.8)
plot(g2)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Quantify V family clonal usage by sample and isotype
family <- countGenes(ExampleDb, gene="v_call", groups=c("sample_id", "c_call"),
clone="clone_id", mode="family")
head(family, n=4)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Subset to IGHM and IGHG for plotting
family <- filter(family, c_call %in% c("IGHM", "IGHG"))
# Plot V family clonal usage by sample and isotype
g3 <- ggplot(family, aes(x=gene, y=clone_freq)) +
theme_bw() +
ggtitle("Clonal Usage") +
theme(axis.text.x=element_text(angle=45, hjust=1, vjust=1)) +
ylab("Percent of repertoire") +
xlab("") +
scale_y_continuous(labels=percent) +
scale_color_brewer(palette="Set1") +
geom_point(aes(color=sample_id), size=5, alpha=0.8) +
facet_grid(. ~ c_call)
plot(g3)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Calculate V family copy numbers by sample and isotype
family <- countGenes(ExampleDb, gene="v_call", groups=c("sample_id", "c_call"),
mode="family", copy="duplicate_count")
head(family, n=4)
## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Subset to IGHM and IGHG for plotting
family <- filter(family, c_call %in% c("IGHM", "IGHG"))
# Plot V family copy abundance by sample and isotype
g4 <- ggplot(family, aes(x=gene, y=copy_freq)) +
theme_bw() +
ggtitle("Copy Number") +
theme(axis.text.x=element_text(angle=45, hjust=1, vjust=1)) +
ylab("Percent of repertoire") +
xlab("") +
scale_y_continuous(labels=percent) +
scale_color_brewer(palette="Set1") +
geom_point(aes(color=sample_id), size=5, alpha=0.8) +
facet_grid(. ~ c_call)
plot(g4)
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