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more hot fixes for demo #33

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Jun 25, 2024
Merged

more hot fixes for demo #33

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28 changes: 20 additions & 8 deletions inst/rmarkdown/templates/rnaseq/skeleton/QC/QC_nf-core.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@ output:
editor_options:
chunk_output_type: console
params:
# params_file: params_qc_nf-core-example.R # example data
# Fill this file with the right paths to nfcore output
params_file: params_qc_nf-core.R
# Put hg38, mm10, mm39, or other
genome: hg38
Expand Down Expand Up @@ -266,9 +268,10 @@ metrics %>%
geom_bar(stat = "identity") +
coord_flip() +
scale_y_continuous(name = "million reads") +
scale_x_discrete(limits = rev) +
scale_fill_cb_friendly() + xlab("") +
ggtitle("Total reads") +
geom_hline(yintercept=20000000, color = "grey", size=2)
geom_hline(yintercept=20000000, color = "grey", linewidth=2)

metrics %>%
ggplot(aes(x = .data[[factor_of_interest]],
Expand Down Expand Up @@ -299,10 +302,11 @@ metrics %>%
color = .data[[factor_of_interest]])) +
geom_point(alpha = 0.5, size=4) +
coord_flip() +
scale_x_discrete(limits = rev) +
scale_color_cb_friendly() +
ylim(0, 100) +
ggtitle("Mapping rate") + xlab("") +
geom_hline(yintercept=70, color = "grey", size=2)
geom_hline(yintercept=70, color = "grey", linewidth=2)
```


Expand Down Expand Up @@ -330,17 +334,19 @@ ggplot(metrics,aes(x = factor(sample, level = order),
geom_bar(stat = "identity") +
coord_flip() +
scale_fill_cb_friendly() +
scale_x_discrete(limits = rev) +
ggtitle("Number of genes") +
ylab("Number of genes") +
xlab("") +
geom_hline(yintercept=20000, color = "grey", size=2)
geom_hline(yintercept=20000, color = "grey", linewidth=2)

metrics %>%
ggplot(aes(x = .data[[factor_of_interest]],
y = n_genes,
color = .data[[factor_of_interest]])) +
geom_point(alpha = 0.5, size=4) +
coord_flip() +
scale_x_discrete(limits = rev) +
scale_y_continuous(name = "million reads") +
scale_color_cb_friendly() + xlab("") +
ggtitle("Number of Genes")
Expand Down Expand Up @@ -377,11 +383,12 @@ metrics %>%
geom_point(alpha = 0.5, size=4) +
ylab("Exonic rate %") +
ggtitle("Exonic mapping rate") +
scale_x_discrete(limits = rev) +
scale_color_cb_friendly() +
coord_flip() +
xlab("") +
ylim(c(0,100)) +
geom_hline(yintercept=70, color = "grey", size=2)
geom_hline(yintercept=70, color = "grey", linewidth=2)
```

## Intronic mapping rate
Expand All @@ -396,11 +403,12 @@ metrics %>%
geom_point(alpha = 0.5, size=4) +
ylab("Intronic rate %") +
ggtitle("Intronic mapping rate") +
scale_x_discrete(limits = rev) +
scale_color_cb_friendly() +
coord_flip() +
xlab("") +
ylim(c(0,100)) +
geom_hline(yintercept=20, color = "grey", size=2)
geom_hline(yintercept=20, color = "grey", linewidth=2)
```

## Intergenic mapping rate
Expand All @@ -416,9 +424,10 @@ metrics %>%
ylab("Intergenic rate %") +
ggtitle("Intergenic mapping rate") +
coord_flip() + xlab("") +
scale_x_discrete(limits = rev) +
scale_color_cb_friendly() +
ylim(c(0, 100)) +
geom_hline(yintercept=15, color = "grey", size=2)
geom_hline(yintercept=15, color = "grey", linewidth=2)
```

## tRNA/rRNA mapping rate
Expand All @@ -437,9 +446,10 @@ metrics %>%
ylim(0, rrna_ylim) +
ggtitle("tRNA/rRNA mapping rate") +
coord_flip() +
scale_x_discrete(limits = rev) +
scale_color_cb_friendly() +
ylim(c(0, 100)) + xlab("") +
geom_hline(yintercept=10, color = "grey", size=2)
geom_hline(yintercept=10, color = "grey", linewidth=2)
```

## 5'->3' bias
Expand All @@ -454,9 +464,10 @@ metrics %>%
geom_point(alpha = 0.5, size=4) +
ggtitle("5'-3' bias") +
coord_flip() +
scale_x_discrete(limits = rev) +
ylim(c(0.5,1.5)) + xlab("") + ylab("5'-3' bias") +
scale_color_cb_friendly()+
geom_hline(yintercept=1, color = "grey", size=2)
geom_hline(yintercept=1, color = "grey", linewidth=2)
```

## Counts per gene - all genes
Expand All @@ -479,6 +490,7 @@ ggplot(counts, aes(factor(name, level = order),
log2(counts+1),
fill = .data[[factor_of_interest]])) +
geom_boxplot() +
scale_x_discrete(limits = rev) +
scale_fill_cb_friendly() +
coord_flip() + xlab("") +
ggtitle("Counts per gene, all non-zero genes") +
Expand Down
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