RectChr | level visualization of genomic statistical variables | Data Visualization library
kandi X-RAY | RectChr Summary
kandi X-RAY | RectChr Summary
RectChr 主要用于基于Chr染色体水平上多层次的可视工具,对一些统计变量用 点,形状,线,柱状和heatmap、高亮,文本文字,彩虹链接, 泛连接,自链接,动态heatmap,动态hist以及结合颜色【即线,散点,直方图,热图,文本, line, scatter/point,shape, histogram , PairWiseLink,link.LinkS,heatmapAnimated,histAnimated, heatmap(highlights)和text 】等 可视化各chr上各区域这个统计量,达到快速一眼看出规律,识别结果。 并且各种可以自己组合 自由修改相关参数,使用方法极像circos的一样。 简单点说 circos 可以画的,这儿均可以画,只是把圈圈图改为长方型的。其中自己搭配层颜色等,同时也比circos多了一些默认配置,用起来十分简单,如SNP GC密度 直接输入文件即可。 可以画遗传图谱,binmap,基因组共线性,GC分布,群体遗传等选择区域,GWAS等等图.程序仅提供11实例. 程序是给一些有基础的生信朋友用的,若是小白看不懂就算了。 RectChr is mainly used for muti-Level visualization tools based on the Chr chromosome level. It uses points,shape, lines, histogram and heatmap, highlighting, text, link,LinkS,heatmapAnimated,histAnimated and PairWiseLink combined colors for some statistical variables [line, scatter, histogram, heatmap, text , line, scatter/point, histogram, PairWiseLink, link,LinkS, heatmap (highlights) and text,heatmapAnimated,histAnimated] and so on to visualize the statistics of each area on each chr, so as to quickly see the pattern and recognize the results at a glance. And various parameters can be combined freely to modify related parameters, and the usage method is very similar to circos. To put it simply, circos can be drawn, and all can be drawn here,but the circle diagram is changed to a rectangular shape. Among them, the color of the layer is matched by itself. At the same time, there are some more default configurations than circos, which is very simple to use, such as SNP GC density and input the file directly. You can draw genetic maps, binmaps, genome collinearity, GC distribution, population genetics and other selected regions, GWAS, etc. The program only provides 11 examples.
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RectChr Key Features
RectChr Examples and Code Snippets
Usage: RectChr -InConfi in.cofi -OutPut OUT
-InConfi : InPut Configuration File
-OutPut : OutPut svg file result
-help See more help *Manual.pdf
Community Discussions
Trending Discussions on Data Visualization
QUESTION
I have the following network graph:
...ANSWER
Answered 2022-Mar-30 at 04:35You could just update relations
using complete
, and than filter out the rows where from
is equal to to
, which gives arrows from a node to itself.
QUESTION
I am working with the R programming language.
I generated the following random data set in R and made a plot of these points:
...ANSWER
Answered 2022-Mar-15 at 17:00You can order your data like so:
QUESTION
I made the following 25 network graphs (all of these graphs are copies for simplicity - in reality, they will all be different):
...ANSWER
Answered 2022-Mar-03 at 21:12While my solution isn't exactly what you describe under Option 2
, it is close. We use combineWidgets()
to create a grid with a single column and a row height where one graph covers most of the screen height. We squeeze in a link between each widget instance that scrolls the browser window down to show the following graph when clicked.
Let me know if this is working for you. It should be possible to automatically adjust the row size according to the browser window size. Currently, this depends on the browser window height being around 1000px.
I modified your code for the graph creation slightly and wrapped it in a function. This allows us to create 25 different-looking graphs easily. This way testing the resulting HTML file is more fun! What follows the function definition is the code to create a list
of HTML objects that we then feed into combineWidgets()
.
QUESTION
I am working with the R programming language. I made the following 3 Dimensional Plot using the "plotly" library:
...ANSWER
Answered 2022-Mar-04 at 17:52You were almost there.
The contours on z
should be defined according to min
-max
values of z
:
QUESTION
I'm trying to build a doughnut chart with rounded edges only on one side. My problem is that I have both sided rounded and not just on the one side. Also can't figure out how to do more foreground arcs not just one.
...ANSWER
Answered 2022-Feb-28 at 08:52The documentation states, that the corner radius is applied to both ends of the arc. Additionally, you want the arcs to overlap, which is also not the case.
You can add the one-sided rounded corners the following way:
- Use arcs
arc
with no corner radius for the data. - Add additional
path
objectscorner
just for the rounded corner. These need to be shifted to the end of eacharc
. - Since
corner
has rounded corners on both sides, add aclipPath
that clips half of this arc. TheclipPath
contains apath
for everycorner
. This is essential for arcs smaller than two times the length of the rounded corners. raise
all elements ofcorner
to the front and thensort
them descending by index, so that they overlap the right way.
QUESTION
Over here (Directly Adding Titles and Labels to Visnetwork), I learned how to directly add titles to graphs made using the "visIgraph()" function:
...ANSWER
Answered 2022-Feb-25 at 10:55Please find below one possible solution.
Reprex
- Your data
QUESTION
In d3
, we may change the order of elements in a selection, for example by using raise
.
Yet, when we rebind the data and use join
, this order is discarded.
This does not happen when we use "the old way" of binding data, using enter
and merge
.
See following fiddle where you can click a circle (for example the blue one) to bring it to front. When you click "redraw", the circles go back to their original z-ordering when using join
, but not when using enter
and merge
.
Can I achive that the circles keep their z-ordering and still use join
?
ANSWER
Answered 2022-Feb-18 at 23:13join
does an implicit order
after merging the enter- and update-selection, see https://github.com/d3/d3-selection/blob/91245ee124ec4dd491e498ecbdc9679d75332b49/src/selection/join.js#L14.
The selection order after the data binding in your example is still red, blue, green even if the document order is changed. So the circles are reordered to the original order using join
.
You can get around that by changing the data binding reflecting the change in the document order. I did that here, by moving the datum of the clicked circle to the end of the data array.
QUESTION
Is there a way to put text along a density line, or for that matter, any path, in ggplot2? By that, I mean either once as a label, in this style of xkcd: 1835, 1950 (middle panel), 1392, or 2234 (middle panel). Alternatively, is there a way to have the line be repeating text, such as this xkcd #930 ? My apologies for all the xkcd, I'm not sure what these styles are called, and it's the only place I can think of that I've seen this before to differentiate areas in this way.
Note: I'm not talking about the hand-drawn xkcd style, nor putting flat labels at the top
I know I can place a straight/flat piece of text, such as via annotate
or geom_text
, but I'm curious about bending such text so it appears to be along the curve of the data.
I'm also curious if there is a name for this style of text-along-line?
Example ggplot2 graph using annotate(...)
:
Above example graph modified with curved text in Inkscape:
Edit: Here's the data for the first two trial runs in March and April, as requested:
...ANSWER
Answered 2021-Nov-08 at 11:31Great question. I have often thought about this. I don't know of any packages that allow it natively, but it's not terribly difficult to do it yourself, since geom_text
accepts angle
as an aesthetic mapping.
Say we have the following plot:
QUESTION
I do realize this has already been addressed here (e.g., matplotlib loop make subplot for each category, Add a subplot within a figure using a for loop and python/matplotlib). Nevertheless, I hope this question was different.
I have customized plot function pretty-print-confusion-matrix
stackoverflow & github. Which generates below plot
I want to add the above-customized plot in for loop to one single plot as subplots.
...ANSWER
Answered 2022-Jan-04 at 09:09Okay so I went through the library's github repository and the issue is that the figure and axes objects are created internally which means that you can't create multiple plots on the same figure. I created a somewhat hacky solution by forking the library. This is the forked library I created to do what you want. And here is a an example piece of code:
QUESTION
I would like to generate a hexagonal lattice heat-map in which each cell represents a group. Likewise, each cell would be a hexagon with a unique color (fill
, set by a column color
in the data-frame) value, and a saturation (alpha
) value corresponding to continuous decimal values from a chemical concentration dateset.
I would like to use a standardized data format which would allow me to quickly construct figures based on standardized datasets containing 25 groups.
For example, a datasheet would look like this:
...ANSWER
Answered 2021-Dec-22 at 01:52If you're open to creating the plot in Python, the following approach would work:
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