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library(tidyverse)Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
had status 1── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0 ✔ purrr 0.3.5
✔ tibble 3.1.8 ✔ dplyr 1.0.10
✔ tidyr 1.2.1 ✔ stringr 1.4.1
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()library(plotly)
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layoutlibrary(ggpubr)
library(rtracklayer)Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:plotly':
rename
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:tidyr':
expand
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:plotly':
slice
The following objects are masked from 'package:dplyr':
collapse, desc, slice
The following object is masked from 'package:purrr':
reduce
Loading required package: GenomeInfoDblibrary(GenomicRanges)myoMyo.gb <- import.gff("../../data/gff/GCA_014108235.1_mMyoMyo1.p_genomic.gff.gz")
df.myoMyo.gb <- rtracklayer::as.data.frame(myoMyo.gb) %>% as_tibble
myoMyo.gb.genes <- df.myoMyo.gb %>% filter(type == 'gene')
myoVel.toga <- import.gff("../../analyses/makeHub/data/gff_temp/gff_temp/mMyoVel1/mMyoVel1_TOGA_hg38.gff")
df.myoVel.toga <- rtracklayer::as.data.frame(myoVel.toga) %>% as_tibble
myoVel.toga.genes <- df.myoVel.toga %>% filter(type == 'gene')p.myoMyo.genbank.hist <- myoMyo.gb.genes %>%
ggplot(
aes(
x=width,
label=ID
)
) +
geom_histogram(binwidth = 1000) +
labs(x='Size(kb)', y='# Genes (log)', title='mMyoMyo - GenBank') +
scale_y_log10() +
theme_pubclean()
p.myoMyo.genbank.hist %>% ggplotly()Warning: The following aesthetics were dropped during statistical transformation: label
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?Warning: Transformation introduced infinite values in continuous y-axisp.myoVel.toga.hist <- myoVel.toga.genes %>%
ggplot(
aes(
x=width,
label=ID
)
) +
geom_histogram(binwidth = 1000) +
scale_y_log10() +
labs(x='Size(kb)', y='# Genes (log)', title='mMyoVel1 - TOGA') +
theme_pubclean()
p.myoVel.toga.hist %>% ggplotly()Warning: The following aesthetics were dropped during statistical transformation: label
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?Warning: Transformation introduced infinite values in continuous y-axisp.overlay.myoVel.myoMyo.hist <- ggplot(
) +
geom_histogram(aes(
x=width,
color=source,
fill=source
),
data= myoVel.toga.genes, binwidth = 1000) +
geom_histogram(aes(
x=width,
color=source,
fill=source
),
data= myoMyo.gb.genes, binwidth = 1000) +
scale_y_log10() +
scale_color_brewer() +
scale_fill_brewer() +
labs(x='Size(kb)', y='# Genes (log)', title='myoMyo GB vs myoVel TOGA') +
theme_pubclean()
p.overlay.myoVel.myoMyo.hist %>% ggplotly()Warning: Transformation introduced infinite values in continuous y-axis
Transformation introduced infinite values in continuous y-axis
sessionInfo()R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] rtracklayer_1.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.7
[4] IRanges_2.32.0 S4Vectors_0.36.1 BiocGenerics_0.44.0
[7] ggpubr_0.4.0 plotly_4.10.1 forcats_0.5.2
[10] stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5
[13] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
[16] ggplot2_3.4.0 tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] googledrive_2.0.0 colorspace_2.0-3
[3] ggsignif_0.6.4 rjson_0.2.21
[5] ellipsis_0.3.2 rprojroot_2.0.3
[7] XVector_0.38.0 fs_1.5.2
[9] rstudioapi_0.14 fansi_1.0.3
[11] lubridate_1.9.0 xml2_1.3.3
[13] codetools_0.2-18 cachem_1.0.6
[15] knitr_1.40 jsonlite_1.8.3
[17] workflowr_1.7.0 Rsamtools_2.14.0
[19] broom_1.0.1 dbplyr_2.2.1
[21] compiler_4.2.2 httr_1.4.4
[23] backports_1.4.1 assertthat_0.2.1
[25] Matrix_1.5-1 fastmap_1.1.0
[27] lazyeval_0.2.2 gargle_1.2.1
[29] cli_3.4.1 later_1.3.0
[31] htmltools_0.5.4 tools_4.2.2
[33] gtable_0.3.1 glue_1.6.2
[35] GenomeInfoDbData_1.2.9 Rcpp_1.0.9
[37] carData_3.0-5 Biobase_2.58.0
[39] cellranger_1.1.0 jquerylib_0.1.4
[41] vctrs_0.5.0 Biostrings_2.66.0
[43] crosstalk_1.2.0 xfun_0.34
[45] rvest_1.0.3 timechange_0.1.1
[47] lifecycle_1.0.3 restfulr_0.0.15
[49] rstatix_0.7.0 XML_3.99-0.13
[51] googlesheets4_1.0.1 zlibbioc_1.44.0
[53] scales_1.2.1 hms_1.1.2
[55] promises_1.2.0.1 MatrixGenerics_1.10.0
[57] parallel_4.2.2 SummarizedExperiment_1.28.0
[59] RColorBrewer_1.1-3 yaml_2.3.6
[61] sass_0.4.2 stringi_1.7.8
[63] BiocIO_1.8.0 BiocParallel_1.32.5
[65] rlang_1.0.6 pkgconfig_2.0.3
[67] bitops_1.0-7 matrixStats_0.63.0
[69] lattice_0.20-45 evaluate_0.18
[71] labeling_0.4.2 GenomicAlignments_1.34.0
[73] htmlwidgets_1.6.1 tidyselect_1.2.0
[75] magrittr_2.0.3 R6_2.5.1
[77] generics_0.1.3 DelayedArray_0.24.0
[79] DBI_1.1.3 pillar_1.8.1
[81] haven_2.5.1 withr_2.5.0
[83] abind_1.4-5 RCurl_1.98-1.10
[85] modelr_0.1.9 crayon_1.5.2
[87] car_3.1-1 utf8_1.2.2
[89] tzdb_0.3.0 rmarkdown_2.17
[91] grid_4.2.2 readxl_1.4.1
[93] data.table_1.14.4 git2r_0.30.1
[95] reprex_2.0.2 digest_0.6.30
[97] httpuv_1.6.6 munsell_0.5.0
[99] viridisLite_0.4.1 bslib_0.4.1