Comments (9)
outlace
commented on May 28, 2024
1
Thanks so much! And oh I'm not computing confidence intervals for the observed data, although I maybe I could using a bootstrapping procedure, maybe I should try that... I'm merely trying to add standard deviation bars to the expected bars which are generated from a null model.
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krassowski
commented on May 28, 2024
1
@VirtualSpaceman you did all well, it is just that there were many changes since version 0.4.0 and that code does not work any more. I will look into that.
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krassowski
commented on May 28, 2024
Thank you! Sure, I would approach it like this:
upset(
observed, sets,
base_annotations=list(
'Intersection size'=upset_annotate(
'..count..',
list(
geom_bar(
aes(fill='observed'),
width=0.35,
position=position_nudge(x=-0.2)
),
geom_bar(
data=expected,
aes(fill='expected'),
width=0.35,
position=position_nudge(x=+0.2)
)
)
)
)
)As an exmple:
observed = data.frame(
a=c(TRUE, FALSE, FALSE, TRUE, TRUE),
b=c(TRUE, TRUE, TRUE, FALSE, TRUE),
c=c(FALSE, TRUE, TRUE, FALSE, FALSE),
d=c(FALSE, FALSE, TRUE, FALSE, FALSE)
)
sets = c('a', 'b', 'c', 'd')then if you have expected counts as a list, create a data frame (each intersection is represented as hyphenated character/string):
expected_summary = data.frame(
exepcted_count=c(
'a-b'=3,
'b-c-d'=1,
'b-c'=1,
'a'=0
)
)
expected_summary$intersection = rownames(expected_summary)
expected_summary
and transform to counts format:
expected = expected_summary[
rep(seq_len(nrow(expected_summary)), expected_summary$exepcted_count),
1:2
]
expected
You can get the intersections data using upset_data() on your data.
Would that work for you?
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outlace
commented on May 28, 2024
Yes I think that will work. Thanks so much for the quick reply.
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outlace
commented on May 28, 2024
I got it working with my data, thanks again! One last thing. I'm having a hard time adding a geom_errorbar to the expected bars. When I add it gets added to the set intersection dot part on the bottom.
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krassowski
commented on May 28, 2024
This is due to the order the plots are assembled - the "dots matrix" is the last one added. With multi-pane plot I had to create a bit different interface (inspired by ComplexHeatmap among others) which requires to specify where the geom should be added. For geom bars one could do:
intersections_data = upset_data(observed, sets)
intersection_sizes = unique(
intersections_data$with_sizes[, c('intersection', 'intersection_size')]
)
intersection_sizes
confidence_intervals = binom::binom.confint(
intersection_sizes$intersection_size,
nrow(observed),
method='wilson'
)
confidence_intervals$intersection = intersection_sizes$intersection
confidence_intervals
upset(
observed, sets,
base_annotations=list(
'Intersection size'=upset_annotate(
'..count..',
list(
geom_bar(
aes(fill='observed'),
width=0.35,
position=position_nudge(x=-0.2)
),
geom_bar(
data=expected,
aes(fill='expected'),
width=0.35,
position=position_nudge(x=+0.2)
),
geom_errorbar(
data=confidence_intervals,
aes(
ymin=lower * nrow(observed),
ymax=upper * nrow(observed),
y=NULL # overwrite the default y=..count...
),
width=0.2,
position=position_nudge(x=-0.2)
)
)
)
)
)
It might be also interesting to apply this to intersection ratios.
Can you share how you calculate the confidence intervals? I would be curious to learn!
I just saw that you mention the expected bars (which might make more sense) - but the relevant code is easy to adjust I guess.
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outlace
commented on May 28, 2024
Hmm would there be a way to directly enter the intersect size counts for my expected bar? When trying to add the SEMs as a geom_errorbar the ymin/max arrays need to be as long as the input observation data which doesn't make sense to me. I have 62 bars for 62 different set intersections but it wont let me put in an array of length 62.
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krassowski
commented on May 28, 2024
Sorry, I cannot see where lies the problem. I would be happy to help if you
can provide a reproducible example.
…On Wed, 6 May 2020, 06:38 Brandon B, ***@***.***> wrote:
Hmm would there be a way to directly enter the intersect size counts for
my expected bar? When trying to add the SEMs as a geom_errorbar the
ymin/max arrays need to be as long as the input observation data which
doesn't make sense to me. I have 62 bars for 62 different set intersections
but it wont let me put in an array of length 62.
—
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VirtualSpaceman
commented on May 28, 2024
Hi,
I tried to reproduce the exact plot according to Mike's instructions and code, but I couldn't. I'm getting the output in below.
As this issue is from last year, maybe some internals have changed and this way doesn't work anymore. As I'm a newcomer in R programming language, I would like to ask: which modifications should I do to reproduce the double bar plot?
Thanks.
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Related Issues (20)
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