Closed crazyhottommy closed 6 years ago
I fixed this bug one week ago. Please update the package.
> mat = normalizeToMatrix(states, tss, value_column = "states_simplified", extend = 10000, w = 200)
> mat
Normalize states to tss:
Upstream 10000 bp (50 windows)
Downstream 10000 bp (50 windows)
Include target regions (width = 1)
720 target regions
signal is categorical (7 levels)
> dim(mat)
[1] 720 100
Thanks! this is working. but somehow the top_annotation
is added automatically even if I did not specify it and the legend is showing the numbers 1,2,...15 rather than the names:e.g. Active TSS.
map = c(
"E1" = "Active TSS",
"E2" = "Flanking Active TSS",
"E3" = "Transcr. at gene 5\' and 3\'",
"E4" = "Strong transcription",
"E5" = "Weak transcription",
"E6" = "Genic enhancers",
"E7" = "Active enhancers",
"E8" = "Trivalent/poised TSS",
"E9" = "Bivalent/poised TSS",
"E10" = "Repressed TSS/Enh",
"E11" = "Repressed Polycomb",
"E12" = "Low",
"E13" = "Artifacts"
)
> devtools::session_info()
Session info -----------------------------------------------------------------------------------------------------
setting value
version R version 3.4.2 (2017-09-28)
system x86_64, darwin15.6.0
ui RStudio (1.0.153)
language (EN)
collate en_US.UTF-8
tz America/Chicago
date 2018-05-07
Packages ---------------------------------------------------------------------------------------------------------
package * version date source
assertthat 0.2.0 2017-04-11 cran (@0.2.0)
base * 3.4.2 2017-10-04 local
bindr 0.1 2016-11-13 cran (@0.1)
bindrcpp 0.2 2017-06-17 cran (@0.2)
Biobase 2.36.2 2017-05-04 cran (@2.36.2)
BiocGenerics * 0.22.1 2017-10-07 cran (@0.22.1)
BiocParallel 1.10.1 2017-05-03 cran (@1.10.1)
Biostrings 2.44.2 2017-07-21 cran (@2.44.2)
bitops 1.0-6 2013-08-17 cran (@1.0-6)
circlize 0.4.3 2017-12-20 cran (@0.4.3)
cli 1.0.0 2017-11-05 CRAN (R 3.4.2)
colorspace 1.3-2 2016-12-14 cran (@1.3-2)
compiler 3.4.2 2017-10-04 local
ComplexHeatmap * 1.17.1 2017-10-25 Github (jokergoo/ComplexHeatmap@de010e6)
crayon 1.3.4 2017-09-16 CRAN (R 3.4.1)
datasets * 3.4.2 2017-10-04 local
DelayedArray 0.2.7 2017-06-03 cran (@0.2.7)
devtools 1.13.3 2017-08-02 CRAN (R 3.4.1)
digest 0.6.15 2018-01-28 cran (@0.6.15)
dplyr 0.7.4 2017-09-28 cran (@0.7.4)
EnrichedHeatmap * 1.9.4 2018-04-06 Github (jokergoo/EnrichedHeatmap@0411ef1)
GenomeInfoDb * 1.12.3 2017-10-05 cran (@1.12.3)
GenomeInfoDbData 0.99.0 2017-10-09 Bioconductor
GenomicAlignments 1.12.2 2017-08-19 cran (@1.12.2)
GenomicRanges * 1.28.6 2017-10-04 cran (@1.28.6)
GetoptLong 0.1.6 2017-03-07 cran (@0.1.6)
GlobalOptions 0.0.13 2018-03-15 cran (@0.0.13)
glue 1.2.0 2017-10-29 cran (@1.2.0)
graphics * 3.4.2 2017-10-04 local
grDevices * 3.4.2 2017-10-04 local
grid * 3.4.2 2017-10-04 local
hms 0.3 2016-11-22 CRAN (R 3.4.0)
IRanges * 2.10.5 2017-10-08 cran (@2.10.5)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.2)
locfit 1.5-9.1 2013-04-20 CRAN (R 3.4.0)
magrittr 1.5 2014-11-22 cran (@1.5)
Matrix 1.2-11 2017-08-21 CRAN (R 3.4.2)
matrixStats 0.53.1 2018-02-11 cran (@0.53.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.2 2017-10-04 local
parallel * 3.4.2 2017-10-04 local
pillar 1.2.1 2018-02-27 cran (@1.2.1)
pkgconfig 2.0.1 2017-03-21 cran (@2.0.1)
png 0.1-7 2013-12-03 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
RColorBrewer 1.1-2 2014-12-07 cran (@1.1-2)
Rcpp 0.12.16 2018-03-13 cran (@0.12.16)
RCurl 1.95-4.8 2016-03-01 cran (@1.95-4.)
readr * 1.1.1 2017-05-16 CRAN (R 3.4.0)
rjson 0.2.15 2014-11-03 cran (@0.2.15)
rlang 0.2.0 2018-02-20 CRAN (R 3.4.3)
Rsamtools 1.28.0 2017-04-25 cran (@1.28.0)
rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)
rtracklayer * 1.36.5 2017-10-04 cran (@1.36.5)
S4Vectors * 0.14.7 2017-10-08 cran (@0.14.7)
shape 1.4.4 2018-02-07 cran (@1.4.4)
stats * 3.4.2 2017-10-04 local
stats4 * 3.4.2 2017-10-04 local
SummarizedExperiment 1.6.5 2017-09-29 cran (@1.6.5)
tibble 1.4.2 2018-01-22 cran (@1.4.2)
tools 3.4.2 2017-10-04 local
utf8 1.1.3 2018-01-03 cran (@1.1.3)
utils * 3.4.2 2017-10-04 local
withr 2.1.1.9000 2018-03-05 Github (jimhester/withr@5d05571)
XML 3.98-1.9 2017-06-19 cran (@3.98-1.)
XVector 0.16.0 2017-04-25 cran (@0.16.0)
zlibbioc 1.22.0 2017-04-25 cran (@1.22.0)
I am sorry for the late reply. I am on a long vocation.
That was a bug I recently made. Now I have updated the package and please update it.
From some version of the package (I cannot remember which), the top annotation is added by default. You can turn it off by setting top_annotation = NULL
.
Thx!
Hi Zuguang,
Thanks for looking into it.
Tommy