ComplexHeatmap | Make Complex Heatmaps | Data Visualization library
kandi X-RAY | ComplexHeatmap Summary
kandi X-RAY | ComplexHeatmap Summary
Make Complex Heatmaps
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of ComplexHeatmap
ComplexHeatmap Key Features
ComplexHeatmap Examples and Code Snippets
Community Discussions
Trending Discussions on ComplexHeatmap
QUESTION
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 10:57I'm not particularly familiar with the package, but do you just want to:
QUESTION
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 08:57Instead 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.
QUESTION
I am trying to create a heatmap with an external dendrogram using the ComplexHeatmap
library .
ANSWER
Answered 2022-Feb-04 at 11:21The problem is that after all the transformations:
QUESTION
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 18:10I figured out the answer to this: I had simply missed adding the side argument to anno_mark as follows:
QUESTION
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 14:47I 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
.
QUESTION
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 13:45From ?ComplexHeatmap::Legend
:
pch
: Type of points if points are used as legend. Note you can use single-letter aspch
, 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:
QUESTION
I'm following the tutorial to make circular plots in R. Suppose I have this dataset:
...ANSWER
Answered 2021-Jul-28 at 03:11Had the same issue with CRAN
version, but it was rectified after installing the dev version
QUESTION
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 08:05You 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
.
QUESTION
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 18:05The only solution I could find is to use the row_split
parameter to put a row into it's own group.
QUESTION
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 18:20See 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.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install ComplexHeatmap
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page