ComplexHeatmap | Make Complex Heatmaps | Data Visualization library

 by   jokergoo R Version: 1.99.4 License: Non-SPDX

kandi X-RAY | ComplexHeatmap Summary

kandi X-RAY | ComplexHeatmap Summary

ComplexHeatmap is a R library typically used in Analytics, Data Visualization, D3 applications. ComplexHeatmap has no bugs, it has no vulnerabilities and it has medium support. However ComplexHeatmap has a Non-SPDX License. You can download it from GitHub.

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              ComplexHeatmap has a medium active ecosystem.
              It has 1074 star(s) with 203 fork(s). There are 37 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 99 open issues and 939 have been closed. On average issues are closed in 69 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of ComplexHeatmap is 1.99.4

            kandi-Quality Quality

              ComplexHeatmap has 0 bugs and 0 code smells.

            kandi-Security Security

              ComplexHeatmap has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              ComplexHeatmap code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              ComplexHeatmap 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.

            kandi-Reuse Reuse

              ComplexHeatmap releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.
              It has 138 lines of code, 0 functions and 1 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

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            ComplexHeatmap Key Features

            No Key Features are available at this moment for ComplexHeatmap.

            ComplexHeatmap Examples and Code Snippets

            No Code Snippets are available at this moment for ComplexHeatmap.

            Community Discussions

            QUESTION

            How to pass unknown variables to another function in R
            Asked 2022-Apr-17 at 10:57

            I am writing a function, which generates a Heatmap using some input data, but performs some transformations beforehand. To generate the actual heatmap, I am using ComplexHeatmap::Heatmap, which offers a huge variety of options to modify the heatmap. I would like to give the user the opportunity to directly specify arguments of the ComplexHeatmap::Heatmap through my functions.

            Right now I am using something which looks like this:

            ...

            ANSWER

            Answered 2022-Apr-17 at 10:57

            I'm not particularly familiar with the package, but do you just want to:

            Source https://stackoverflow.com/questions/71901226

            QUESTION

            inner labelling for heatmap, in R ggplot
            Asked 2022-Feb-26 at 09:02

            I am trying to add a number label on each cell of a heatmap. Because it also needs marginal barcharts I have tried two packages. iheatmapr and ComplexHeatmap.

            (1st try) iheatmapr makes it easy to add to add bars as below, but I couldnt see how to add labels inside the heatmap on individual cells.

            ...

            ANSWER

            Answered 2022-Feb-26 at 08:57

            Instead of relying on packages which offer out-of-the-box solutions one option to achieve your desired result would be to create your plot from scratch using ggplot2 and patchwork which gives you much more control to style your plot, to add labels and so on.

            Note: The issue with iheatmapr is that it returns a plotly object, not a ggplot. That's why you can't use ggsave.

            Source https://stackoverflow.com/questions/71275092

            QUESTION

            External dendrogram does not keep the same formation when using it for cluster_rows in complexheatmap
            Asked 2022-Feb-04 at 11:21

            I am trying to create a heatmap with an external dendrogram using the ComplexHeatmap library .

            ...

            ANSWER

            Answered 2022-Feb-04 at 11:21

            The problem is that after all the transformations:

            Source https://stackoverflow.com/questions/70956152

            QUESTION

            ComplexHeatmap change direction of segment/link in rowAnnotation
            Asked 2022-Jan-03 at 18:10

            I am building a large heatmap and have added a row annotation. This particular annotation must be on the left side of the heatmap, but when I add labels, the segment/link is facing the wrong direction. Can someone help me figure out how to flip the segment to be in between the label and the annotation?

            Reproducible example:

            ...

            ANSWER

            Answered 2022-Jan-03 at 18:10

            I figured out the answer to this: I had simply missed adding the side argument to anno_mark as follows:

            Source https://stackoverflow.com/questions/70526460

            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

            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

            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

            Bray–Curtis distance calculation method in Complexheatmap?
            Asked 2021-Jul-15 at 08:05

            I'm using the Complexheatmap function (or "Heatmap") in R and was wondering if there was a way to use the Bray-Curtis method in calculating col/row distance (with ward.D2 clustering method) since it's not a supported method in Complexheatmap. I need to use this function instead of heatmap.2 and pheatmap, unfortunately.

            Here is some made-up fish count data (My actual data has 47 sites (rows) and 32 seasons, but I wasn't sure how to recreate that here):

            ...

            ANSWER

            Answered 2021-Jul-15 at 08:05

            You should first define a function for Bray-Curtis distance calculation (bray_dist).
            Then, you set clustering_distance_rows=bray_dist and clustering_distance_rows=bray_dist in Heatmap.

            Source https://stackoverflow.com/questions/68291560

            QUESTION

            Complexheatmap highlight specific rows
            Asked 2021-Apr-13 at 22:52

            How can I highlight only specific rows by drawing rectangle around the corresponding cells of the row or by making the row name bold and colored as shown below in the image (pointed to with arrows). Many thanks.

            ...

            ANSWER

            Answered 2021-Mar-26 at 18:05

            The only solution I could find is to use the row_split parameter to put a row into it's own group.

            Source https://stackoverflow.com/questions/65966708

            QUESTION

            How to fix image saving that's cutting off y-axis text in R?
            Asked 2021-Mar-26 at 18:20

            I have a heatmap where the text for the y-axis keeps getting cut off. The text gets cut off whether I try to save the image manually in RStudio export, or using:

            ...

            ANSWER

            Answered 2021-Mar-26 at 18:20

            See my comment above: I think you are talking about the truncated row labels when you say "text for the y-axis". If that is indeed the issue you are struggling with, then increasing the Heatmap parameter row_names_max_width from the default unit(6, "cm") to something like row_names_max_width = unit(12, "cm") should allow you to accommodate longer row labels.

            Source https://stackoverflow.com/questions/66763776

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

            Vulnerabilities

            No vulnerabilities reported

            Install ComplexHeatmap

            ComplexHeatmap is available on Bioconductor, you can install it by:.

            Support

            The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap.
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