Comments (8)
qingxi586
commented on August 10, 2024
1
Thank you wilkox, this is what I want to achieve, thank you very much for your help！
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wilkox
commented on August 10, 2024
Hi @qingxi586, it looks like you might be using the patchwork package to compose the plots? I can show you how to combine the two plots but I need access to the data stored in z and f. Please post your current code as a reprex.
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qingxi586
commented on August 10, 2024
I tried to merge them using the patchwork package, but it was not successful，I will now present my data to you
> z
net TE X_start X_end direction start end
1 Fill Alt.Os0365_LTR_Truncator#LTR/Gypsy 0 619 1 4 620
2 Fill Alt.Os0173_LTR_Dasheng#LTR/Gypsy 0 440 0 620 1061
3 Fill Alt.Os0173_LTR_Dasheng#LTR/Gypsy 0 440 0 7942 8383
4 Fill Alt.Os0365_LTR_Truncator#LTR/Gypsy 614 2282 1 8383 10050
5 Fill Alt.Os0039_LTR_RIRE3#LTR/Gypsy 0 3139 0 10049 13196
6 Fill Alt.Os0039_LTR_RIRE3#LTR/Gypsy 0 3139 0 18964 22115
7 Fill Alt.Os0365_LTR_Truncator#LTR/Gypsy 2278 2989 1 22117 22824
> f
net TE X_start X_end direction start end
1 Fill Alt.Os0173_INT_Dasheng#LTR/Gypsy 713 6310 0 1061 7071
2 Fill Alt.Os0039_INT_RIRE3#LTR/Gypsy 0 5791 0 13196 18963
It can be observed that these coordinates are all continuous, and I want to represent LTR and INT separately with different arrows in a linear gene
and this is my code
(ggplot(z, aes(xmin = start, xmax = end,y = net, fill = TE,forward = direction,label = TE)) + geom_gene_arrow() +ggplot(f, aes(xmin = start, xmax = end,y = net, fill = TE,forward = direction,label = TE)) + geom_gene_arrow(arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm")))+facet_wrap( ~ net,scales = "free", ncol = 1)+theme_genes() +
scale_fill_brewer(palette = "Set3") +labs(title=sv_names)+theme(plot.title = element_text(hjust = 0.5,vjust = -130),axis.text.x = element_text(hjust = 0.5, vjust = 185))+geom_gene_label()
thank you for your help!
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wilkox
commented on August 10, 2024
library(tidyverse)
library(gggenes)
z <- tribble(
~net , ~TE , ~X_start , ~X_end , ~direction , ~start , ~end ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 0 , 619 , 1 , 4 , 620 ,
"Fill" , "Alt.Os0173_LTR_Dasheng#LTR/Gypsy" , 0 , 440 , 0 , 620 , 1061 ,
"Fill" , "Alt.Os0173_LTR_Dasheng#LTR/Gypsy" , 0 , 440 , 0 , 7942 , 8383 ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 614 , 2282 , 1 , 8383 , 10050 ,
"Fill" , "Alt.Os0039_LTR_RIRE3#LTR/Gypsy" , 0 , 3139 , 0 , 10049 , 13196 ,
"Fill" , "Alt.Os0039_LTR_RIRE3#LTR/Gypsy" , 0 , 3139 , 0 , 18964 , 22115 ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 2278 , 2989 , 1 , 22117 , 22824)
z$type <- "LTR"
f <- tribble(
~net , ~TE , ~X_start , ~X_end , ~direction , ~start , ~end ,
"Fill" , "Alt.Os0173_INT_Dasheng#LTR/Gypsy" , 713 , 6310 , 0 , 1061 , 7071 ,
"Fill" , "Alt.Os0039_INT_RIRE3#LTR/Gypsy" , 0 , 5791 , 0 , 13196 , 18963)
f$type <- "INT"
genes <- bind_rows(z, f)
ggplot(genes, aes(xmin = start, xmax = end, y = net, fill = TE,
forward = direction, label = TE)) +
geom_gene_arrow() +
facet_wrap(~ type, scales = "free", ncol = 1) +
theme_genes()
Created on 2024-03-15 with reprex v2.1.0
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qingxi586
commented on August 10, 2024
Hi,wilkox
Maybe there are some issues with my description，The data in z and f are actually together, but I divided INT and LTR into two files. This file originally looked like this
> a
net TE X_start X_end direction start end
1 Fill Alt.Os0365_LTR_Truncator#LTR/Gypsy 0 619 1 4 620
2 Fill Alt.Os0173_LTR_Dasheng#LTR/Gypsy 0 440 0 620 1061
3 Fill Alt.Os0173_INT_Dasheng#LTR/Gypsy 713 6310 0 1061 7071
4 Fill Alt.Os0173_LTR_Dasheng#LTR/Gypsy 0 440 0 7942 8383
5 Fill Alt.Os0365_LTR_Truncator#LTR/Gypsy 614 2282 1 8383 10050
6 Fill Alt.Os0039_LTR_RIRE3#LTR/Gypsy 0 3139 0 10049 13196
7 Fill Alt.Os0039_INT_RIRE3#LTR/Gypsy 0 5791 0 13196 18963
8 Fill Alt.Os0039_LTR_RIRE3#LTR/Gypsy 0 3139 0 18964 22115
9 Fill Alt.Os0365_LTR_Truncator#LTR/Gypsy 2278 2989 1 22117 22824
Using your gggenes package does draw nice arrows，like this
I said before that I wanted to use two different arrows to plot my genes，LTR uses default parameters geom_gene_arrow() , INT uses another parameter geom_gene_arrow(arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm"))
This way I can get the picture I want .
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wilkox
commented on August 10, 2024
I don't think I really understand what you're trying to achieve. Is it something like this?
library(tidyverse)
library(gggenes)
z <- tribble(
~net , ~TE , ~X_start , ~X_end , ~direction , ~start , ~end ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 0 , 619 , 1 , 4 , 620 ,
"Fill" , "Alt.Os0173_LTR_Dasheng#LTR/Gypsy" , 0 , 440 , 0 , 620 , 1061 ,
"Fill" , "Alt.Os0173_LTR_Dasheng#LTR/Gypsy" , 0 , 440 , 0 , 7942 , 8383 ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 614 , 2282 , 1 , 8383 , 10050 ,
"Fill" , "Alt.Os0039_LTR_RIRE3#LTR/Gypsy" , 0 , 3139 , 0 , 10049 , 13196 ,
"Fill" , "Alt.Os0039_LTR_RIRE3#LTR/Gypsy" , 0 , 3139 , 0 , 18964 , 22115 ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 2278 , 2989 , 1 , 22117 , 22824)
z$type <- "LTR"
f <- tribble(
~net , ~TE , ~X_start , ~X_end , ~direction , ~start , ~end ,
"Fill" , "Alt.Os0173_INT_Dasheng#LTR/Gypsy" , 713 , 6310 , 0 , 1061 , 7071 ,
"Fill" , "Alt.Os0039_INT_RIRE3#LTR/Gypsy" , 0 , 5791 , 0 , 13196 , 18963)
f$type <- "INT"
genes <- bind_rows(z, f)
ggplot(genes, aes(xmin = start, xmax = end, y = type, fill = TE,
forward = direction, label = TE)) +
geom_gene_arrow(data = z) +
geom_gene_arrow(data = f, arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm")) +
theme_genes()
Created on 2024-03-17 with reprex v2.1.0
If not, maybe you could draw it on paper and take a picture to show what you want?
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qingxi586
commented on August 10, 2024
Sorry, my description is not accurate enough, I use Adobe illustrator to show you
In this picture you can see Alt.Os0173_INT_Dasheng#LTR/Gypsy and Alt.Os0039_INT_RIRE3#LTR/Gypsy The parameters used are geom_gene_arrow(arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm"))
While other TEs use geom_gene_arrow()
This is what I want to express, I want two different arrows to be drawn on one graph at the same time.
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wilkox
commented on August 10, 2024
Thanks for the picture. Is this what you're after?
library(tidyverse)
library(gggenes)
z <- tribble(
~net , ~TE , ~X_start , ~X_end , ~direction , ~start , ~end ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 0 , 619 , 1 , 4 , 620 ,
"Fill" , "Alt.Os0173_LTR_Dasheng#LTR/Gypsy" , 0 , 440 , 0 , 620 , 1061 ,
"Fill" , "Alt.Os0173_LTR_Dasheng#LTR/Gypsy" , 0 , 440 , 0 , 7942 , 8383 ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 614 , 2282 , 1 , 8383 , 10050 ,
"Fill" , "Alt.Os0039_LTR_RIRE3#LTR/Gypsy" , 0 , 3139 , 0 , 10049 , 13196 ,
"Fill" , "Alt.Os0039_LTR_RIRE3#LTR/Gypsy" , 0 , 3139 , 0 , 18964 , 22115 ,
"Fill" , "Alt.Os0365_LTR_Truncator#LTR/Gypsy" , 2278 , 2989 , 1 , 22117 , 22824)
z$type <- "LTR"
f <- tribble(
~net , ~TE , ~X_start , ~X_end , ~direction , ~start , ~end ,
"Fill" , "Alt.Os0173_INT_Dasheng#LTR/Gypsy" , 713 , 6310 , 0 , 1061 , 7071 ,
"Fill" , "Alt.Os0039_INT_RIRE3#LTR/Gypsy" , 0 , 5791 , 0 , 13196 , 18963)
f$type <- "INT"
genes <- bind_rows(z, f)
ggplot(genes, aes(xmin = start, xmax = end, y = "fill", fill = TE,
forward = direction, label = TE)) +
geom_gene_arrow(data = z) +
geom_gene_arrow(data = f, arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm")) +
theme_genes() +
scale_fill_brewer(palette = "Set3") +
labs(y = "net", title = "MH63.chr01_SV10298075")
Created on 2024-03-19 with reprex v2.1.0
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