Open MarineBergot opened 2 years ago
Hi @MarineBergot , Do you mean from a database? Common CNV/SNV? All we plot in pyGenomeTracks rely on local files. I don't know in which format are encoded SNV/CNV.
Thanks for your super quick answer! no it's local files, with our pipeline we have file with all CNV/SNV in vcf or gvcf format My goal would be to plot area with TAD, gene expression, CNV/SNV and genes
For the moment, we don't support vcf. Could you make a scheme on how you would represent them, so when we have time to develop new features, we know how it could be useful? Meanwhile I guess you can convert the vcf to bed (if you don't know how to do, just do a head of your vcf I will give you the command)...
Hi again ! i'm trying to add CNV to my (not perfect) plot, i have issue with color. I tried to cheat and added color with bed12 but i don't have bed12. i converted vcf to bed with rgb color regarding the type of CNV but i don't know what to put in the 3 last columns then it's not working (i tried with 0 and 1 but no ) my file looks like that :
chr1 43593267 43594572 . 0 . 43593267 43594572 188,100,241 chr1 30195841 218197336 . 0 . 30195841 218197336 188,100,241 chr1 205209141 205210012 . 0 . 205209141 205210012 188,100,241 chr1 237402443 237403261 . 0 . 237402443 237403261 188,100,241 chr1 247146749 247149421 . 0 . 247146749 247149421 188,100,241 chr2 207644871 207645844 . 0 . 207644871 207645844 188,100,241 chr3 44699170 44701119 . 0 . 44699170 44701119 188,100,241 chr3 93470002 93471081 . 0 . 93470002 93471081 188,100,241 chr3 165092497 165093482 . 0 . 165092497 165093482 188,100,241 chr4 49104007 49658148 . 0 . 49104007 49658148 188,100,241
my .ini file
[x-axis] where = top
[hic matrix] file = dijhic008/hicMatrix/dijhic008_50000_merge_norm_correct.h5 title = 50kb dijhic008 chromothripsis
depth = 5000000 transform = log1p file_type = hic_matrix
[tads] file =dijhic008_TADs_50000_merge_domains.bed file_type = domains border_color = black color = none
overlay_previous = share-y
[spacer] height = 0.05
[hic matrix] file = dijhic001_50000_norm_correct.h5 title = 50kb dijhic001 CTRL
depth = 1000000 transform = log1p file_type = hic_matrix
[tads] file = dijhic001_TADs_50000_domains.bed file_type = domains border_color = black color = none
overlay_previous = share-y
[spacer] height = 0.05
[test arcs overlay] file =dijarn085.arc line_width = 3 height=3
[gtf exons]
file = grch38.refseq.with_genes.gtf
height = 10
title = gtf (exons and transcripts)
fontsize = 12
file_type = gtf
prefered_name = gene_name
[CNV] file = dijen080_cnv_bed12.bed height = 7 title = genes (bed12) style = flybase; fontsize = 10; height_utr = 0.7 style = flybase fontsize = 10 height_utr = 0.7
[bigwig] file = ENCFF757LRW.bw color = blue height = 4 title = CTCF min_value = 0 max_value = 30
[vlines] file = genes.bed type = vlines
do you have any idea i could do to have on color regarding the type of CNV? (and how to put my 2 TAD plot on the same scale? ) and if you have something for RNAseq data? like to add some plot for each gene with the number of count to see if the gene is down or up ? sorry for all my asking and thanks again for your incredible help!
Hi,
color = bed_rgb
and I would not put label as they are '.' for all. So it would be:
[CNV]
file = dijen080_cnv_bed12.bed
height = 3
title = CNV
color = bed_rgb
labels = false
merge_transcripts = true
and merge_overlapping_exons = true
.--binSize
option in hicBuildMatrix
. This is why you have 2 different resolutions. What I would do:
a. Run hicInfo -m dijhic008/hicMatrix/dijhic008_50000_merge_norm_correct.h5
to get the resolution of the first matrix.
b. Rerun hicBuildMatrix --samFiles .... --binSize ...
for the second: dijhic001 with the binSize obtained in (a.)
c. Rerun correction and TAD calling on corrected matricescolor = Reds
or any other colormap (https://matplotlib.org/stable/tutorials/colors/colormaps.html).
c. You extract from a DE analysis the log2 fold-change and you generate a bed with this value in the fifth field and you plot this bed with color = bwr
or any other Diverging colormap (https://matplotlib.org/stable/tutorials/colors/colormaps.html#diverging).PS: For the next exchanges, would you mind to put your ini file in a code block? You can generate a code block with triple ` followed by ini:
```ini
your ini file
Thanks
thanks for your quick answer, i tried as you suggested for CNV but nothing is shown :/ this is my bed (i'm supposed to have only one CNV in this area):
chr8 26054488 26055284 None 0 . 26054488 26055284 188,100,241
chr8 43238145 43242668 None 0 . 43238145 43242668 188,100,241
chr8 85261666 85262425 CA13 0 . 85261666 85262425 188,100,241
chr8 72111027 72111742 None~None 0 . 72111027 72111742 242,243,244
chr8 84952812 84953527 None~None 0 . 84952812 84953527 242,243,244
chr8 99145226 99145941 VPS13B~VPS13B 0 . 99145226 99145941 242,243,244
chr8 130897333 130898048 ADCY8~ADCY8 0 . 130897333 130898048 242,243,244
chr8 51817225 51817940 PCMTD1~None 0 . 51817225 51817940 242,243,244
chr8 51818564 51819279 PCMTD1~None 0 . 51818564 51819279 242,243,244
chr8 14488547 14489262 SGCZ~GXYLT1 0 . 14488547 14489262 242,243,244
chr8 15431497 15432212 None~KLF12 0 . 15431497 15432212 242,243,244
chr8 30287528 30288243 None~None 0 . 30287528 30288243 242,243,244
chr8 28576084 28576799 None~None 0 . 28576084 28576799 242,243,244
chr8 133959623 133960338 None~None 0 . 133959623 133960338 242,243,244
chr8 93653916 93654631 LINC00535~None 0 . 93653916 93654631 242,243,244
chr8 643942 649756 ERICH1 0 . 643942 649756 221,20,35
chr8 6111142 6115456 None 0 . 6111142 6115456 221,20,35
chr8 15919242 15930056 None 0 . 15919242 15930056 221,20,35
chr8 25114442 25133956 None 0 . 25114442 25133956 221,20,35
`[x-axis]
where = top
[hic matrix]
file = hicMatrix/dijhic008_25000_merge_norm_correct.h5
title = 25kb dijhic008 chromothripsis
# depth is the maximum distance plotted in bp. In Hi-C tracks
# the height of the track is calculated based on the depth such
# that the matrix does not look deformed
depth = 3000000
transform = log1p
file_type = hic_matrix
max_value=50
[tads]
file = TADs/dijhic008_TADs_25000_merge_domains.bed
file_type = domains
border_color = black
color = none
# the tads are overlay over the hic-matrix
# the share-y options sets the y-axis to be shared
# between the Hi-C matrix and the TADs.
overlay_previous = share-y
[spacer]
height = 0.05
[hic matrix]
file = hicMatrix/dijhic001_25000_norm_correct.h5
title = 25kb dijhic001 CTRL
# depth is the maximum distance plotted in bp. In Hi-C tracks
# the height of the track is calculated based on the depth such
# that the matrix does not look deformed
depth = 3000000
transform = log1p
file_type = hic_matrix
max_value = 50
[tads]
file =TADs/dijhic001_TADs_25000_domains.bed
file_type = domains
border_color = black
color = none
# the tads are overlay over the hic-matrix
# the share-y options sets the y-axis to be shared
# between the Hi-C matrix and the TADs.
overlay_previous = share-y
[spacer]
height = 0.05
[test arcs overlay]
file = TADs/dijarn085.arc
line_width = 3
height=3
[gtf exons]
file =grch38.refseq.with_genes.gtf
height = 12
title = gtf grch38 (exons and transcripts)
fontsize = 12
file_type = gtf
prefered_name = gene_name
[CNV]
file = dijen080_cnv_bed9.bed
height = 3
title = CNV
color = bed_rgb
labels = false
[bigwig]
file = ENCFF757LRW.bw
color = blue
height = 4
title = CTCF
min_value = 0
max_value = 30
`
3) it was supposed to be same bin but after checking, yeah it wasn't, now it's working perfectly thanks 4) i'm experimenting your options i will let you know the results!
edit : CNV worked but scale is not right, apparently the black line is supposed to be my CNV
i tried with other region, do you have any idea how to improve the figure?
What do you mean by 'scale is not right'. In your bed I see:
chr8 643942 649756 ERICH1 0 . 643942 649756 221,20,35
Which is the one you see in your region (chr8:6-11Mb).
If the problem is that you don't see the color, add border_color = bed_rgb
.
If you know the CNV does not overlap, you can put:
[CNV]
file = dijen080_cnv_bed9.bed
height = 1
display = collapsed
title = CNV
color = bed_rgb
border_color = bed_rgb
labels = false
ah it's perfect like that thanks !
H! it's me again :) i'm still working on my plot to add RNA-seq data. I added easily coverage but i would like to add zscore, do you have something like that? i tried with a bedgraph file but nothing is shown, i can't understand why
my file looks like that :
"chr8" 95133784 95156685 -2.51
"chr8" 9555911 9782346 0.44
"chr8" 96222946 96235545 -0.39
"chr8" 96239401 96261610 -0.97
"chr8" 96261901 96336995 -0.4
"chr8" 96493812 96611790 -1.97
"chr8" 96645241 97143501 0.95
"chr8" 97273487 97277928 0.01
"chr8" 97644183 97730260 -0.25
"chr8" 97775787 97853013 -1.05
"chr8" 97869063 98036724 -0.36
"chr8" 98041720 98045545 -0.02
"chr8" 98064567 98093609 1.24
"chr8" 98102343 98117171 -1.38
"chr8" 98117292 98159835 0.65
"chr8" 98189825 98294235 1.04
"chr8" 98454632 98825688 0.42
"chr8" 98944441 98952100 0.09
"chr8" 99013273 99877580 1.37
"chr8" 99877864 99893707 -1.45
my .ici file (beginning didn't change)
[SNV]
file = dijen080_snv.bed
title = SNV
height = 1
display = collapsed
color = bed_rgb
border_color = bed_rgb
[mutations CTCF]
file = mutations_CTCF.bed
title = mutations CTCF
height = 1
display = collapsed
color = bed_rgb
border_color = bed_rgb
[bedgraph RNA-Seq]
file = dijarn085.bedGraph
title = RNA-seq coverage
color = green
width = 0.2
# optional. Default is yes, set to no to turn off the visualization of data range
show data range = yes
# optional, otherwise guessed from file ending
file_type = bedgraph
height = 4
[bedgraph RNA-Seq zscore]
file = TADs/zscore.bg
title = RNA-seq Zscore
color = red
width = 0.2
# optional. Default is yes, set to no to turn off the visualization of data range
show data range = yes
# optional, otherwise guessed from file ending
file_type = bedgraph
height = 4
[bigwig Chipseq]
file = CTCF_data/ENCFF757LRW.bw
color = blue
height = 4
title = CTCF
min_value = 0
max_value = 30
thanks for your help!
Marine
It is because of the quotes around your chromosome name.
me again, i have issue with my CNV. Maybe it's not possible but in case of for future. I have different bed file : -one with CNV -one with SNV -one with CNV/SNV which occured in CTCF sequences
this is really not so good when they are in differents lines, i tried to put everything in same bed but it wasn't good solution apparently.
do you think there is a way to draw with differents colors the differns types of CNV/SNV/CTCF mutations directly on the genes ?
thanks!
and maybe improve arc ?
I need more info to help you:
For the overlay you are asking. There is an option: overlay_previous = yes
which allow to draw one track on top of the other one, for example, TAD on top of heatmap but it can also be CNV on top of genes... I don't know if this helps you.
Hi ! thanks for your work, i would like to know if it's possible to add CNV/SNV on the plot? thanks :)
i'm using: python 3.8 pyGenomeTracks 3.7