8000 display flip flop fix by alphabdiallo · Pull Request #103 · formbio/laava · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

display flip flop fix #103

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 12 commits into
base: main
Choose a base branch
from
Draft

display flip flop fix #103

Changes from all commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
322de8e
display flip flop only for ssAAV
alphabdiallo Jun 4, 2025
1811755
Removing flip flop table for sc
alphabdiallo Jun 5, 2025
71d9a37
Adding sc flipflop logic
Jun 5, 2025
14746db
updating sc flip flop
alphabdiallo Jun 5, 2025
55f2a34
look at the rightITR for scAAV flip flop analysis
alphabdiallo Jun 6, 2025
d866956
Fixing issue with sc flip flop table display
alphabdiallo Jun 6, 2025
5ea0e0d
Fixing sc flexable
alphabdiallo Jun 6, 2025
da4c12f
Printing flextable columns
alphabdiallo Jun 6, 2025
83dc5e2
Deplaxing sc ITR results
alphabdiallo Jun 6, 2025
79fda2c
aggregating counts of same ITR configutation
alphabdiallo Jun 6, 2025
9abbf08
Adding logic to plot flip or flop for fulls and right-partials
alphabdiallo Jun 10, 2025
4caecf2
sc flip and flop only for fulls
alphabdiallo Jun 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
89 changes: 65 additions & 24 deletions src/report.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -543,37 +543,78 @@ if (file.exists(agg_flipflop_tsv)) {

```{r ffplot, message=FALSE, warning=FALSE, results='asis'}
if (exists("df.flipflop") && (nrow(df.flipflop) > 1)) {
# Generate flip/flop summary plot
ffplot <- df.flipflop %>%
mutate(
class = if_else(
leftITR == 'unclassified' | rightITR == 'unclassified',
"unclassified",
paste(leftITR, rightITR, sep = '-')
)
) %>%
mutate(
unclass = if_else( class == "unclassified", "unclassified", "classified")
) %>%
group_by(type, subtype, class, unclass) %>%
summarize(classct = sum(count)) %>%
filter(subtype == 'full')
ggplot(ffplot, aes(x = class, y = classct, fill = unclass)) +
geom_bar(stat = 'identity', show.legend = FALSE) +
labs(x = 'Assigned type') +
scale_y_continuous("Number of reads",
limits = c(0, NA),
expand = expansion(mult = c(0, 0.05)))

if (params$vector_type == "ss") {
# Generate flip/flop summary plot
ffplot <- df.flipflop %>%
mutate(
class = if_else(
leftITR == 'unclassified' | rightITR == 'unclassified',
"unclassified",
paste(leftITR, rightITR, sep = '-')
)
) %>%
mutate(
unclass = if_else( class == "unclassified", "unclassified", "classified")
) %>%
group_by(type, subtype, class, unclass) %>%
summarize(classct = sum(count)) %>%
filter(subtype == 'full')
ggplot(ffplot, aes(x = class, y = classct, fill = unclass)) +
geom_bar(stat = 'identity', show.legend = FALSE) +
labs(x = 'Assigned type') +
scale_y_continuous("Number of reads",
limits = c(0, NA),
expand = expansion(mult = c(0, 0.05)))
} else if (params$vector_type == "sc") {
# Generate flip/flop summary plot
ffplot <- df.flipflop %>%
mutate(
class = if_else(
rightITR == 'unclassified',
"unclassified",
paste(rightITR)
)
) %>%
mutate(
unclass = if_else( class == "unclassified", "unclassified", "classified")
) %>%
group_by(type, subtype, class, unclass) %>%
summarize(classct = sum(count)) %>%
filter(subtype == 'full')
ggplot(ffplot, aes(x = class, y = classct, fill = unclass)) +
geom_bar(stat = 'identity', show.legend = FALSE) +
labs(x = 'Assigned type') +
scale_y_continuous("Number of reads",
limits = c(0, NA),
expand = expansion(mult = c(0, 0.05)))
}
} else {
cat("No flip/flop analysis results available to display.")
}
```

```{r fftable, message=FALSE, warning=FALSE, results='asis'}
if (exists("df.flipflop") && (nrow(df.flipflop) > 1)) {
flextable(df.flipflop) %>%
set_header_labels(values = c("type", "subtype", "leftITR", "rightITR", "count"))
if (params$vector_type == "ss") {
flextable(df.flipflop) %>%
set_header_labels(values = c("type" = "Type", "subtype" = "Subtype", "leftITR" = "Left ITR", "rightITR" = "Right ITR", "count" = "Count"))

}
else if (params$vector_type == "sc") {
# flextable(df.flipflop) %>%
# set_header_labels(values = c("type", "subtype", "leftITR", "rightITR", "count"))
# flextable(df.flipflop) %>%
# set_header_labels(values = c("type", "subtype", "leftITR", "rightITR", "count")) %>%
# select(type, subtype, rightITR, count)
#print(colnames(df.flipflop))
df.flipflop %>%
group_by(type, subtype, rightITR) %>%
summarize(count = sum(count), .groups = "drop") %>%
select(type, subtype, rightITR, count) %>%
filter(subtype == 'full' ) %>%
flextable() %>%
set_header_labels(values = c("type" = "Type", "subtype" = "Subtype", "rightITR" = "Right ITR", "count" = "Count"))
}
}
```

Expand Down
Loading
0