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guigolab / ggsashimi

Command-line tool for the visualization of splicing events across multiple samples
MIT License
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Annotation and density plots are not aligned with ggplot2 version greater than 2.2.1 #6

Closed emi80 closed 6 years ago

emi80 commented 6 years ago

In ggplot2 versions greater that 2.2.1 grobs have a different number of colums

emi80 commented 6 years ago

As discussed with @dgarrimar we could use:

grob$widths[grob$layout$r[grob$layout$name=="axis-l"]]

to select widths for axis-l,ylab-l,background

dgarrimar commented 6 years ago

As discussed with @emi80 and @abreschi, a temporary solution would be to attach to ggplot2 v2.2.1 or use our docker image. We are working to fix this issue as soon as possible.

shinyanishio commented 6 years ago

Hi. To avoid this problem, we download docker image, however same trouble was seen in case with docker images. sashimi 15.39.18.pdf

dgarrimar commented 6 years ago

Hi @shinyanishio, did you build the Docker image yourself from the Dockerfile or got it from DockerHub?

shinyanishio commented 6 years ago

Hi! We are install docker image according with your GitHub page instruction.

git clone https://github.com/guigolab/ggsashimi.git docker pull guigolab/ggsashimi cd ggsashimi docker build -f docker/Dockerfile -t guigolab/ggsashimi . docker run guigolab/ggsashimi --help

After docker image building we tested follow, however annotation fields are not aligned. docker run -w $PWD -v $PWD:$PWD guigolab/ggsashimi -b examples/input_bams.tsv -c chr10:27040584-27048100 -g examples/annotation.gtf -M 10 -C 3 -O 3 --shrink --alpha 0.25 --base-size=20 --ann-height=4 --height=3 --width=18 -P examples/palette.txt

shinyanishio commented 6 years ago

We tried Mac OS 10.13 and Ubuntu 16.04 LTS but both of them are same results.

dgarrimar commented 6 years ago

As it claims in the README, docker pull guigolab/ggsashimi allows you to get the Docker image from DockerHub. It seems that after pulling it you have built a new one on top by running docker build (these steps are alternative). While the former should contain the right version of ggplot2, the latter does not, as the libraries got updated. Just remove the image that you built and run docker pull guigolab/ggsashimi again to get the original container. Then it should work properly!

dgarrimar commented 6 years ago

I updated the README file to clarify this

shinyanishio commented 6 years ago

Thank you for your help!! Now we can draw apropriately !!