circlize

R Circlize, Chord graph with empty sectors

由 丶灬走出姿态 提交于 2020-01-16 00:58:08
问题 I am trying to create a chord graph using the circlize package in R. I would like to include sectors for which there is no outflow (no links emanating from them). Is there a way to: Force the program to report rows from my data frame, even if there are only zeros in that row. Suppress self-loops. (The vignettes calls on you to enter zeros at the diagonal to do this, but then we're back to the first problem.) I have attached my code. chordDiagram(mat, symmetric = TRUE, keep.diagonal = TRUE,

R circlize chord diagram with log scale

由 一世执手 提交于 2019-12-25 07:27:20
问题 Is it possible to make a chord diagram in the circlize package that displays log10 values? So far I have been able to produce a plot with correct size links, but the corresponding axis will not match up. the axis displays the sum of all links/logged values per sector, which is not correct as summing logged values does not correspond to summed raw values. Is there any way to fix this axis problem? below is an example of what I have tried so far library(circlize) export_country <- c("DEU","USA"

Grouping track in the package circlize in R

由 落爺英雄遲暮 提交于 2019-12-23 02:38:36
问题 I have created a plot similar to the one on page 8 of the circlize tutorial here: http://cran.r-project.org/web/packages/circlize/vignettes/genomic_plot.pdf Now I am trying to overlay an additional track on top of the gene names, which shows grouping of the genes into bigger categories (in the image below taken from the vignette, I am trying to add the blue lines, hoping to get a prettier image with circlize). I have a new data frame with the start and stop of each of these wider regions, and

R: Adjusting Labels in circlize diagram

由 China☆狼群 提交于 2019-12-19 11:52:30
问题 I have the code below which im trying to make into a circular diagram using the amazing package circlize I have read the vigenette and admit some of it has gone over my head a bit, I was wondering if there is a quick way to remove all the labels on my diagram including tick marks and just add back in AUDI, VOLVO and BMW in light grey at the same angle to the sector as per this example library (dplyr) library(circlize) df = read.table(textConnection(" Brand_from model_from Brand_to Model_to

R circlize: Error in circos.initialize

由 爷，独闯天下 提交于 2019-12-12 10:30:03
问题 I am able to follow the Circlize example in the description of the package on CRAN easily: library('circlize') set.seed(123) mat = matrix(sample(1:100, 18, replace = TRUE), 3, 6) rownames(mat) = letters[1:3] colnames(mat) = LETTERS[1:6] ### basic settings par(mfrow = c(3, 2)) par(mar = c(1, 1, 1, 1)) chordDiagram(mat) however, when I replace mat with myMatrix I get this error: Error in circos.initialize(factors = factor(cate, levels = cate), xlim = cbind(rep(0, : Since `xlim` is a matrix, it

Rotate labels in a chordDiagram (R circlize)

由 江枫思渺然 提交于 2019-11-30 12:41:30
Here is some code from the circlize package for creating a chord diagram.Right now the labels are parallel to the edge of the circle. Is it possible to rotate the labels 90 degrees to they are perpendicular to the circle? library(circlize) set.seed(999) mat = matrix(sample(18, 18), 3, 6) rownames(mat) = paste0("Start", 1:3) colnames(mat) = paste0("End", 1:6) chordDiagrm(mat) In the figure below I manually inserted a few labels to show what I hope to accomplish (End5, End6, End7). Thanks. Based on your example data, here's one way to do it: grid.col <- setNames(rainbow(length(unlist(dimnames

Rotate labels in a chordDiagram (R circlize)

由 限于喜欢 提交于 2019-11-29 18:57:59
问题 Here is some code from the circlize package for creating a chord diagram.Right now the labels are parallel to the edge of the circle. Is it possible to rotate the labels 90 degrees to they are perpendicular to the circle? library(circlize) set.seed(999) mat = matrix(sample(18, 18), 3, 6) rownames(mat) = paste0("Start", 1:3) colnames(mat) = paste0("End", 1:6) chordDiagrm(mat) In the figure below I manually inserted a few labels to show what I hope to accomplish (End5, End6, End7). Thanks. 回答1:

R make circle/chord diagram with circlize from dataframe

由 我只是一个虾纸丫 提交于 2019-11-28 17:40:27
I would like to make a chord diagram using the circlize package . I have a dataframe containing cars with four columns. The 2 first columns contains information on car band and model owned and the next two columns to the brand and model the respondent migrated to. Here is a simple example of the dataframe: Brand_from model_from Brand_to Model_to 1: VOLVO s80 BMW 5series 2: BMW 3series BMW 3series 3: VOLVO s60 VOLVO s60 4: VOLVO s60 VOLVO s80 5: BMW 3series AUDI s4 6: AUDI a4 BMW 3series 7: AUDI a5 AUDI a5 It would be great to be able to make this into a chord diagram. I found an example in the

R make circle/chord diagram with circlize from dataframe

由 守給你的承諾、 提交于 2019-11-27 10:38:56
问题 I would like to make a chord diagram using the circlize package . I have a dataframe containing cars with four columns. The 2 first columns contains information on car band and model owned and the next two columns to the brand and model the respondent migrated to. Here is a simple example of the dataframe: Brand_from model_from Brand_to Model_to 1: VOLVO s80 BMW 5series 2: BMW 3series BMW 3series 3: VOLVO s60 VOLVO s60 4: VOLVO s60 VOLVO s80 5: BMW 3series AUDI s4 6: AUDI a4 BMW 3series 7:
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