hello. TickingClock1992!

First of all, thank you for making good use of your package.
As a personal problem, I had to use the source code as a copy paste instead of installing the RIdeogram package, but I was able to confirm the following error.

Error in rescale(mydata$Value, to = c(1, cnum)) :
could not find function "rescale"
Calls: ideogram
Execution halted

I confirmed that the function called rescale is inside the scales package, and the above pacakage is installed in R in the server.

However, the above message was continuously output, and as a result of running it with R-studio, it worked normally as a result of taking it out to a window to see if it was a problem with the source itself.

It seems that ##' @importFrom scales rescale is not loaded properly, but I can't think of a solution, so I would like to ask for help.

My server environment is Ubuntu and R is version 3.6.0.
The R Studio that I took out to Windows and checked is version 4.2.0.
(window = version 10)
Could you please let me know what the problem is?

Thank you in advance

Hi,

I wonder if there is an easy way to add text as label in addition or instead of a symbol?

Thanks!

Thanks for this good tool. I am new for this software and can you give some information of how to make the input file for synteny analysis, I mean transfer the resulted .collinearity file from MCScanX into RIdeogram because the file from MCScan have no chromosome info. Many thanks.

Hello, I am trying to display an overlay of 235592 specific markers, but I am getting an error when converting the SVG to PNG:

convertSVG("chromosome.svg", device = "png")
Error in rsvg_format(svg, file, width = width, height = height, css = css, :
Failed to parse svg: XML parse error: cannot load more than 200000 XML elements

Is there a way to overcome this?
Thanks

Hello.

I am trying to run:

require(RIdeogram)
library(devtools)

karyotype <- read.table('karyotype.txt', header = T)
synteny <- read.table('synteny.txt', header = T)

ideogram(karyotype = karyotype, synteny = synteny)

My files look like:
karyotype.txt
Chr Start End fill species size color
Myx_Chr22 1 47849308 139b08 B 9.5 139b08
Myx_Chr43 1 38023304 139b08 B 9.5 139b08
Myx_Chr27 1 46332826 078dd8 A 9.5 078dd8
Myx_Chr42 1 38410338 078dd8 A 9.5 078dd8

synteny.txt
Chr1 start1 end1 Chr2 start2 end2
22 14531668 14595454 27 32941637 32994325
22 14811096 15022136 27 32437958 32709008
22 15667970 15705569 27 31616867 31646678
...

When I run this code I get this error:

Error in [<-.data.frame(tmp, i, 8, value = c(B = NA_real_)) :
new columns would leave holes after existing columns

I am just trying to understand what is going on.

Thank you for your time.

How does this program package customize the spacing of chromosomes? I hope to get your reply，thank you.

Hi!
I am trying to install RIdeogram. First, I typed
library(devtools)
to load devtools package in the workspace, then I tried to install RIdeogam this way:
devtools::install_github('TickingClock1992/RIdeogram').
I get this error:

Error in library.dynam(lib, package, package.lib) :
shared object ‘colorspace.so’ not found

Obviously, I tried to:

• re-install the package colorspace (with dep=T)
• remove the package colorspace and install once again

but the outcome did not change, the error was the same.
My R version is 4.2.0, I don't know if it's important.
Thank you for tour time,
Giuseppe

尊敬的作者：
你好！我在画图过程中发现正常生成的SVG文件打不开，打开后是xml的格式并没有出现图画，转化为PNG也是出错只转化了一部分。
这是这两个文件。

期望的图是中间有共线性线条的

希望作者大大帮帮忙~，谢谢！

Hi there!

I'm trying to load in my GFF file using the function GFFex but it keeps coming up with the following error:
Error in seq.default(0, subset(karyotype, karyotype$Chr == names(list_chr[i]))[1, : 'to' must be a finite number

I was wondering what I could do to rectify this.

Here are the chromosome and GFF files that I am using. Thanks!!
Archive.zip

Dear Zhaodong Hao,

thank you so much for this software!
I was wondering if there is any way to plot an ideogram where the bands inside it represent genes colored by metabolic categories instead of the gene density.

I was thinking perhaps something like this:

Chr |Start | End | Color
contig_1 | 40968 | 42014 | 9EBF91
contig_1 | 99302 | 101028 | 56A6BA
contig_2 | 487948 | 491187 | 56A6BA

etc.

Where the color is characteristic of a particular metabolic category, COG genes for instance. Even the ideogram without a legend would be ok, because the legend could be easily made by hand.

Thank you so much!

L.

Where can I download the starting and ending positions of mouse centromeres？The genome version is mm10,thank you.

I use "label = Zea_DEGs, label_type = "marker"" to plot, but Error occured: C stack usage 15926272 is too close to the limit

when I use RIdeogram, I found it draws picture from up to down. so the start position is above the stop position. but the start position of different chromosomes is not on the same horizontal line， so It is impossible to draw a Y-axis for physical distance. Is there any parameter can be used to make drawing from down to up. so that all chromosomes start at botton. and I can draw Y-axis by myself. thanks.

Hello, I am running into this error when trying to add labels:

Error in if (label_type == "marker") { : argument is of length zero

It might be a newbie question but I'm stuck, so sorry for asking. Here is the command I run and the 3 files that are fed to R-Studio (attached):
files.zip

ideogram(karyotype = Book4[,1-3], label = single, overlaid = 4xdead)

Dear Ticking Clock,

When I use RIdeogram to create plots, I came across C stack error as following:

Loading required package: RIdeogram
Error: C stack usage  7971108 is too close to the limit
Execution halted

Could you please help me with this problem?

Best regards,
Jiajian ZHOU
Ph.D.
Southern Medical University, China

I was able to install the package/visualize the sample data correctly, however the dual synteny plotter is hitting an error with my custom data. I can visualize my ideogram file alone, which makes me thing the problem is the synteny data frame. I head that below and show the error.

`> head(xtrm.dual)
Species_1 Start_1 End_1 Species_2 Start_2 End_2 fill
1 4 1217548 1218572 8078 25642678 25642943 ccccc
2 7 77444663 77457538 8134 58786633 58830026 ccccc
3 9 68868221 68871184 561 142495507 142515248 ccccc
4 3 136956088 136957125 7757 290722045 290804997 ccccc
5 3 70399900 70405443 4870 308049357 308056384 ccccc
6 10 50635257 50638250 8134 133443259 133454068 ccccc

ideogram(karyotype = xtrm.ideo, synteny = xtrm.dual)
Error in if (synteny[i, 1] == "1") synteny[i, 8] <- 3.5 * 35.43307 + synteny[i, :
missing value where TRUE/FALSE needed`

I am attaching the two data files used to generate the data. I will say using the read.table command provided was not sufficient for the above message, I tried to set the columns in my data to have the same class as the sample data, but that just changed from an undefined error to the current one.

xt.rm.dualcomp.txt
trop.rana.4ideogram.txt

Dear,

I was trying to visualize AD GWAS result following the tutorial on the website, while there comes an error that C stack usage 7972308 is too close to the limit, it works for the first 20 lines but not more, I didn't find useful solutions, have you encounter this one?
sig_Jansen_2019_snps_hg38.txt

Best,
Peng

Dear Hao,
Thanks for the nice tool first. As mentioned in the title, I would like to ask how to draw both intra- and interspecies synteny blocks, such as Figure 1d in the Liriodendron genome paper?

Hi:
So useful package this is !
However, I have some annotion data like ：

1 3000500 3136999 -0.338434787450111
1 37321500 37489499 -0.533675006500781
1 37510500 37673999 -0.567659305780682
1 49247000 49471999 -0.781532436705488
1 153160500 153286999 -0.275541774503734

The range of fourth column is -0.9,0.5 ,and I want to set 0 as the midpoint of colours，Ideogram seems to set the mean as the midpoint of colours.
Could you give me some advice ?
Thanks in advance !

I've tried the following with this karyotype file:

devtools::install_github('TickingClock1992/RIdeogram')

require(RIdeogram)

setwd('/home/juan/Desktop/juan/bio/svevo-zavitan')
data(human_karyotype, package="RIdeogram")
data(gene_density, package="RIdeogram")

human_karyotype
gene_density

karyo = read.csv(file="data/karyotype.csv", header=TRUE, sep=",")
density = read.csv(file="data/snp_dens.csv", header=TRUE, sep=",")

ideogram(karyotype = karyo, overlaid = density)
convertSVG("chromosome.svg", device = "png")

Chr,Start,End,CE_start,CE_end
chr1A,0,585266722,0,0
chr1B,0,681112512,0,0
chr2A,0,775448786,0,0
chr2B,0,790338525,0,0
chr3A,0,746673839,0,0
chr3B,0,836514780,0,0
chr4A,0,736872137,0,0
chr4B,0,676292951,0,0
chr5A,0,669155517,0,0
chr5B,0,701372996,0,0
chr6A,0,615672275,0,0
chr6B,0,698614761,0,0
chr7A,0,728031845,0,0
chr7B,0,722970987,0,0
chrUn,0,498719471,0,0

and got the following error:

ideogram(karyotype = karyo, overlaid = density)
Error in nchar(karyotype$Chr) : 'nchar()' requires a character vector

So I have to modify my karyotype as follow:

Chr,Start,End,CE_start,CE_end
1,0,585266722,0,0
2,0,681112512,0,0
3,0,775448786,0,0
4,0,790338525,0,0
5,0,746673839,0,0
6,0,836514780,0,0
7,0,736872137,0,0
8,0,676292951,0,0
9,0,669155517,0,0
10,0,701372996,0,0
11,0,615672275,0,0
12,0,698614761,0,0
13,0,728031845,0,0
14,0,722970987,0,0
15,0,498719471,0,0

Would be nice to support the other format

Hi Developer,

I want to display a specific area with a bar.
For example, I want to display the coordinates such as the position of repeat and the position of heterochromatin with a bar on the chromosome diagram.

In other words, I want to plot information like # 2 with a bar against information on chromosomes like # 1.
Does your tool make this possible?

1

Chr Start End
1 0 187018787
2 0 158822865
3 0 134443407
4 0 125483849
5 0 124558973

2

Chr Start End
1 112636 112700
1 519847 519940
1 635196 635250
1 741262 741317
1 815333 815417
1 1228350 1228404
1 129134729 129134800
1 129842726 129842850
1 129886838 129886900
1 130945692 130945749
1 131086596 131086650
1 131671866 131671938

Best regards,

The top legend overlaps with the plot, can I move it elsewhere?

hi there, thanks for this package.

This is really great. I'm interested to create graphics to display ancestry information, something like https://github.com/jordanlab/tagore

Is this something that can be achieved?

Thanks

Dear Hao,
Thank you for the useful package RIdeogram.
I couldn't find any parameter to create an horizontal ideogram instead of the default vertical.
Also I wanted to increase the font size of the labels. Are these options implemented yet in the package?

Best regards,
Julien

I want to use horizontal view, not sure if there is any ways to rotate the chromosomes. Thank you!

Hi, thanks s o much for the nice plotting tool! I really like it. I have been successfully generate my chromosome-shape ideogram. Now I would like to use the synteny function to draw a synteny plot.

I know RIdeogram can do that, but I would like to add panels such as GC content, gene density and so on on top of the synteny plot, rather than in the chromosome-shape ideogram. May I ask how I should do it? I guess the code should be more or less similar to the chromosome-shape one? Many thanks in advance!

Hi Developer,
I want to add some text labels to underline some gene just like:

But I didn't find parameters for it.If there is an easy way for that?
Thanks!

Hi,

Thank you for the nice RIdeogram software. It is indeed difficult to find good and easy to use software for plotting synteny between 2 linear maps. This is what I hope that Rideogram can do.

I got the examples to work and also got some of my own data into a 2 way synteny plot.

I wonder how the connection is made between chromosomes in karyotype and synteny file?

In the the example code (also shown below) Roman numerals are used to identify the chromosomes in the karyotype file. In my own file I used chrX and lgX in this file. I am comparing a genetic and physical map.

In the synteny file normal (Arabic) numerals are used, and also required, otherwise the software runs into an error.

How does Rideogram know on which chromosome from the karytype file a line from the synteny file should be plotted? The chromosome names don't match up.

Is it also possible to manually line up the order of chromosomes between 2 maps?
For example I know that chr1 corresponds to lg7 in my case, and the plot would be much nicer if chr1 and lg7 are direct below/above each other. Maybe even better with a straight instead of a curved line. Some chromosomes / linkage group maps could also be flipped, to get them in the same orientation (this is something that I also could do manually of course).

Thank you.

data(karyotype_dual_comparison, package="RIdeogram")
head(karyotype_dual_comparison)
#>   Chr Start      End   fill species size  color
#> 1  I      1 23037639 969696   Grape   12 252525
#> 2  II     1 18779884 969696   Grape   12 252525
#> 3 III     1 19341862 969696   Grape   12 252525
#> 4  IV     1 23867706 969696   Grape   12 252525
#> 5   V     1 25021643 969696   Grape   12 252525
#> 6  VI     1 21508407 0ab276   Grape   12 252525
table(karyotype_dual_comparison$species)
#> 
#>   Grape Populus 
#>      19      19

data(synteny_dual_comparison, package="RIdeogram")
head(synteny_dual_comparison)
#>   Species_1  Start_1    End_1 Species_2 Start_2   End_2   fill
#> 1         1 12226377 12267836         2 5900307 5827251 cccccc
#> 2        15  5635667  5667377        17 4459512 4393226 cccccc
#> 3         9  7916366  7945659         3 8618518 8486865 cccccc
#> 4         2  8214553  8242202        18 5964233 6027199 cccccc
#> 5        13  2330522  2356593        14 6224069 6138821 cccccc
#> 6        11 10861038 10886821        10 8099058 8011502 cccccc

Hi,

Can I use this program to visualise where my small RNA-seq reads map to my genome?

Thank you in advance for answering me:-)

Have a nice day.

Hi,

Thanks for developing such a convenient tool, can you add ruler information on one side?

Thanks
Shenglong

So I am comparing gene positions in 3 different genomes (different plant ecotypes of the same species). I would love to have the nice display of the 3 genomes in a pyramid-like graph with the lines connecting the 1:1 orthologs from species A to B and from A to C (A being the "best reference" among the 3 genomes).

I managed to produce the input files without any error and the figure nicely displays pretty much want I want, but it seems like all the connector lines have "shifted" or "skewed" end positions. I see 2 issues more specifically :

1. Some lines beginning in species A end up in between 2 chromosomes in species B or C. How is that possible ? It's difficult to estimate where these shifted lines should end up (i.e. in which of the 2 chromosomes these lines should finish?).
2. A possibly related issue is that multiple connector lines end up way beyond the end of the last chromosome in both species B and C. Could this be related to the fact that all the lines are shifted? Is it because I have too many 1:1 orthology relationships and the connector line density is too high to output all the lines at the right position? Here you have the image for reference:

I was wondering how this issue could be solved. I triple checked and all the positions in the synteny file are right. There is no start or end position in any of the genes that extends beyond the last position of the last chromosome. All the positions are correct, so I assume that it must be related to the way the lines are outputted in the package. But maybe I'm wrong... Could I play with some parameters to extend the little colored boxes that represent the chromosomes so that the line fits the good positions ?

I've attached my karyotype and synteny files for reference as well. Just in case it can help solving the problem.

Thanks so much for any help. I like that package, so I hope we can come up with a solution.
csat.synteny_ternary.chrom-only.txt
csat.karyotype_ternary.txt

Hello, can you add a chromosome length ruler to this R package?

Hi,

Thanks for working on this nice package.

I am wondering if there is a way to produce the ideogram corresponding to a specific region of interest. Say, one is only interested in displaying the left arm of chromosome 1. How would you achieve that?

Thanks

Hello, could you add a "lable" length scale to this R package? the finall result as following.