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Improve plotAbundance #156

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merged 38 commits into from
Nov 1, 2024
Merged

Improve plotAbundance #156

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TuomasBorman Oct 8, 2024
2964549
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TuomasBorman Oct 8, 2024
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TuomasBorman Oct 8, 2024
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TuomasBorman Oct 8, 2024
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TuomasBorman Oct 8, 2024
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TuomasBorman Oct 9, 2024
2ba9675
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TuomasBorman Oct 9, 2024
4dc5405
Fix bioccheck
TuomasBorman Oct 9, 2024
8af0bc3
update tests
TuomasBorman Oct 9, 2024
7a3eece
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TuomasBorman Oct 9, 2024
c950ebb
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TuomasBorman Oct 9, 2024
711ecfa
remove warnings
TuomasBorman Oct 9, 2024
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TuomasBorman Oct 9, 2024
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TuomasBorman Oct 9, 2024
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TuomasBorman Oct 9, 2024
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TuomasBorman Oct 9, 2024
fa78ac8
Merge branch 'devel' into plotabundance_mods
TuomasBorman Oct 9, 2024
aa59828
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TuomasBorman Oct 9, 2024
ce13f56
little bugfix
Daenarys8 Oct 14, 2024
6bff303
fix deps
Daenarys8 Oct 14, 2024
1407f0a
fix deps
Daenarys8 Oct 14, 2024
952df9b
Support variables with spaces
TuomasBorman Oct 17, 2024
07142a0
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TuomasBorman Oct 22, 2024
c755a44
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TuomasBorman Oct 22, 2024
6277a10
bugfix
TuomasBorman Oct 22, 2024
14ca525
Remove support for spaces.
TuomasBorman Oct 22, 2024
a0ad64e
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TuomasBorman Oct 22, 2024
bad9567
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TuomasBorman Oct 22, 2024
f23b312
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TuomasBorman Oct 24, 2024
12ac4aa
add bar layout
Daenarys8 Oct 28, 2024
b814727
update
Daenarys8 Oct 28, 2024
99803e1
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TuomasBorman Oct 29, 2024
146af91
Merge branch 'devel' into plotabundance_mods
TuomasBorman Nov 1, 2024
cdd5c07
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TuomasBorman Nov 1, 2024
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TuomasBorman Nov 1, 2024
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TuomasBorman Nov 1, 2024
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2 changes: 1 addition & 1 deletion R/plotAbundance.R
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Expand Up @@ -237,7 +237,7 @@ setMethod("plotAbundance", signature = c("SummarizedExperiment"), function(
# agglomeration and transformation. The outut is a single tibble with all the
# whole dataset for plotting.
.get_abundance_data <- function(
x, assay.type, layout, group = rank, rank = NULL,
x, assay.type, layout = "bar", group = rank, rank = NULL,
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as.relative = use_relative, use_relative = FALSE, ...){
# Input check
if( !(is.null(group) || (
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