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robinweide / GENOVA

GENome Organisation Visual Analytics
GNU General Public License v3.0
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Labels in visualise #233

Open MarijneMia opened 3 years ago

MarijneMia commented 3 years ago

Describe the bug The labels in visualise for the apa discovery has inverted labels for the y axis in the top row.

To Reproduce library(GENOVA)

pl <- read.delim('your_favorite_loops.bed') WT_10kb_hicpro <- load_contacts(signal_path = "WT_10kb_iced.matrix", indices_path = "WT_10kb_abs.bed", sample_name = "WT", colour = "black")

apa <- APA(explist = list("WT" = WT_10kb_hicpro), bedpe = pl) visualise(apa)

Expected behavior I would expect the "-100 kb" label towards the top, and the "100 kb" label towards the bottom of the APA matrix.

Screenshots image

deWitLab commented 3 years ago

The reason is that the diagonal is in the bottomleft corner. This means that positions closer to the diagonal are considered “upstream” of the loop. I assume that this is why these position are considered negative.

Best, Elzo

On 17 Nov 2020, at 14:40, MarijneMia notifications@github.com<mailto:notifications@github.com> wrote:

Describe the bug The labels in visualise for the apa discovery has inverted labels for the y axis in the top row.

To Reproduce library(GENOVA)

pl <- read.delim('your_favorite_loops.bed') WT_10kb_hicpro <- load_contacts(signal_path = "WT_10kb_iced.matrix", indices_path = "WT_10kb_abs.bed", sample_name = "WT", colour = "black")

apa <- APA(explist = list("WT" = WT_10kb_hicpro), bedpe = pl) visualise(apa)

Expected behavior I would expect the "-100 kb" label towards the top, and the "100 kb" label towards the bottom of the APA matrix.

Screenshots [image]https://user-images.githubusercontent.com/24277124/99396666-4fb64f80-28e2-11eb-9976-3bc06091afdd.png

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robinweide commented 3 years ago

The reason is that the diagonal is in the bottomleft corner. This means that positions closer to the diagonal are considered “upstream” of the loop. I assume that this is why these position are considered negative.

This. But let see if more people are annoyed by this.