robinweide
Labels in visualise
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
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 <[email protected]mailto:[email protected]> 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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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.
