circlize | Circular visualization in R | Graphics library

by jokergoo R Version: 0.2.5 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | circlize Summary

circlize is a R library typically used in User Interface, Graphics applications. circlize has no bugs, it has no vulnerabilities and it has medium support. However circlize has a Non-SPDX License. You can download it from GitHub.

Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.

Support

Quality

Security

License

Reuse

Support

circlize has a medium active ecosystem.

It has 856 star(s) with 135 fork(s). There are 27 watchers for this library.

It had no major release in the last 6 months.

There are 35 open issues and 317 have been closed. On average issues are closed in 113 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of circlize is 0.2.5

Quality

circlize has 0 bugs and 0 code smells.

Security

circlize has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

circlize code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

circlize has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

circlize releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

It has 17864 lines of code, 0 functions and 126 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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circlize Key Features

No Key Features are available at this moment for circlize.

circlize Examples and Code Snippets

No Code Snippets are available at this moment for circlize.

Community Discussions

Trending Discussions on circlize

R package circlize: circos heatmap colors not showing up

how to give different color for the lines in the Sankey plot to show different groups?

Values for asterisks incorrectly placed on heat map

Confusion matrix using table in k-means and hierarchical clustering

Put labels inside the legend color bar in circlize chord diagram

Using circlize::draw.sectors inside a function

circos.heatmap(): Error in rowMeans(m) : 'x' must be an array of at least two dimensions

Add percentage labels inside bars in circos.barplot in Circlize

Use circos function in circos

Changing the legend in complex heatmap

QUESTION

R package circlize: circos heatmap colors not showing up

Asked 2022-Mar-16 at 20:49

I am trying to create a circular plot using circlize package. When using hex color codes, my plot does not show up anything but when I use actual color names, it shows. Why is that?

Code:

...

ANSWER

Answered 2022-Mar-16 at 20:43

According to the docs, when describing the argument col

If the values are characters, the color should be a named color vector.

Whereas you are passing a list rather than a named vector. So if you unlist col_fun1 (or create it with c() instead of list()), you get

Source https://stackoverflow.com/questions/71503731

QUESTION

how to give different color for the lines in the Sankey plot to show different groups?

Asked 2021-Dec-03 at 18:46

I have a question on this Sankey plot in R. So basically I want to give different color for the line that connect the source and target nodes based on the variable group. Below are the codes I found from one of the R platform. Essentially the code give you the plot but the connecting line are similar in color. My question is how to give different color for the lines to know that specific group is represented in specific color.

Thank you! Best AD

...

ANSWER

Answered 2021-Dec-02 at 16:59

Following the example from the networkD3::sankeyNetwork documentation you could add a links variable to the data and set the LinkGroup argument...

Source https://stackoverflow.com/questions/70198927

QUESTION

Values for asterisks incorrectly placed on heat map

Asked 2021-Nov-10 at 14:47

I want to put asterisks in the heat map for P-values < 0.05. I have a separate spreadsheet with the P-values that I read into R and subsequently the heat map, however, the function i'm using doesn't seem to place the asterisks in the right cells. In the Figure below, for example, there are no P-values attached to the rho = 0 cells, and yet there are asterisks placed there.

Spreadsheet is shown below. For all P-values that are NA, I put in "1" to avoid an error. If there's a better way to do this on top of fixing the placements of the asterisks, please let me know.

The code that i'm using is as follows:

...

ANSWER

Answered 2021-Nov-10 at 14:47

I managed to fix this by removing the first column of labels in the spreadsheet and re-running the code. I think that converting the data frame as a matrix would give further assurance per this example. The issue with my code was that the order of sx_syn was not the same as sx_syn_p.

Source https://stackoverflow.com/questions/69904360

QUESTION

Confusion matrix using table in k-means and hierarchical clustering

Asked 2021-Oct-07 at 15:14

I have some problems with calculating of confusion matrix. I have created three sets of points by multivariate normal distibution:

...

ANSWER

Answered 2021-Oct-07 at 15:14

Using your data, insert set.seed(42) just before you create sigma1 so that we have a reproducible example. Then after you created X:

Source https://stackoverflow.com/questions/69472378

QUESTION

Put labels inside the legend color bar in circlize chord diagram

Asked 2021-Jul-29 at 16:58

I've been following the circular visualization in R tutorial.

I try to recreate the figure in Chapter 16 A complex example of Chord diagram. Particularly, I am asking on how to make the labelled legend for 'Chromatin States', i.e. to label each box in the color legend with numbers.

The text refers to the legend section ("Legends can be added according to instructions discussed in Section 4"). However, labelling inside individual legend grids is not explicitly described there.

Below is the codes to the data:

...

ANSWER

Answered 2021-Jul-29 at 13:45

From ?ComplexHeatmap::Legend:

pch: Type of points if points are used as legend. Note you can use single-letter as pch, e.g. pch = 'A'

background: Background colors for the grids. It is used when points and lines are the legend graphics.

Thus, one possibilty may be to use type = "points instead of the default "grid"; create the labels as pch = as.character(). As background, use your state_col vector. Small example:

Source https://stackoverflow.com/questions/68570867

QUESTION

Using circlize::draw.sectors inside a function

Asked 2021-Jul-29 at 01:23

I would like to make a RGB color scheme using the circlize package. First, I try to make a function so that I only have to input the color and sectors, and the function will do the job

Here is the code:

...

ANSWER

Answered 2021-Jul-29 at 01:23

Update: I managed to run the function:

Source https://stackoverflow.com/questions/68546094

QUESTION

circos.heatmap(): Error in rowMeans(m) : 'x' must be an array of at least two dimensions

Asked 2021-Jul-28 at 03:11

I'm following the tutorial to make circular plots in R. Suppose I have this dataset:

...

ANSWER

Answered 2021-Jul-28 at 03:11

Had the same issue with CRAN version, but it was rectified after installing the dev version

Source https://stackoverflow.com/questions/68553336

QUESTION

Add percentage labels inside bars in circos.barplot in Circlize

Asked 2021-May-12 at 17:22

I was able to create a stacked bar chart like this:

...

ANSWER

Answered 2021-May-12 at 17:22

I figured it out by modifying the code of the circos.barplot function.

The labels are drawn in a second loop after the rectangles so that the rectangles are not drawn over the labels.

Source https://stackoverflow.com/questions/67504090

QUESTION

Use circos function in circos

Asked 2021-May-03 at 05:17

Can someone help me ? How can I add my circos function in my data? when i try i get an error message and it doesn't produce any results I want to do a donut figure like the representation number 1 but i have one other resultat that we can see in the other picture. Trying to follow this guide

My data is lile this :

...

ANSWER

Answered 2021-May-03 at 05:17

Your example data is significantly different to the "nba" examples you have used in this and previous questions. This is why you are having so much trouble. Here are three ways to visualize your actual data:

1.) Tidyverse geom_tile() method:

Source https://stackoverflow.com/questions/67342060

QUESTION

Changing the legend in complex heatmap

Asked 2021-Jan-10 at 21:30

With this code I have this complexheatmap

...

ANSWER

Answered 2021-Jan-10 at 21:30

Heatmap(mat, border = T, show_column_names = F,
        rect_gp = gpar(col = "white", lwd = 1),
        column_split = response$response, 
        col = c("-2" = "blue", "0" = "grey", "1" = "red"),
        heatmap_legend_param = list(at = c("-2", "0", "1"), labels = c("Del", "Netral", "Amp")),
        show_column_dend = F,
        show_row_dend = F,
        left_annotation = left_annotation,
        right_annotation = right_annotation,name = "CNV",
        row_names_gp = gpar("fontface" = "italic")
)

Source https://stackoverflow.com/questions/65657662

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install circlize

The package can be installed from CRAN:.

Support

The full documentations are available at https://jokergoo.github.io/circlize_book/book/ and the online website is at https://jokergoo.github.io/circlize/.

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