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Questions tagged [gplots]

Various R programming tools for plotting data

gplots: Various R programming tools for plotting data

164 questions
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Changing line width of dendrogram in heatmap.2

I'm trying to plot a heatmap using gplots::heatmap.2() .There are a lot of rows and the dendrogram lines appear to be quite thin compared to the image. I 'm wondering if there is any technique to thicken the dendrogram lines as mentioned in this…
The August
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Textbox in gridarrange

I am arranging two graphs on a pdf using grid.arrange. I would like to have a text box between the title and the first plot to add some information on the graphs themselves possibly editing in in rich text. What is the best solution for that? I…
MCS
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How to edit digits inside a venn diagram in Rstudio

I want to visualise true-positives and true-negatives using a venn diagram. Is it possible to edit the "digits" given inside the venn diagram? I have made a normal venn diagram in R, using gplots. One of the circle has True-positive and…
RonnB
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In `gplots` in `R`, how can we adjust the position of the x-label ticks in the `heatmap.2` function?

I am trying to duplicate a plot found here on pg. 4: The reproducible code for it is: require(devtools) install_git("https://github.com/marchion/git.switchBox", subdir="switchBox") require(switchBox) require(gplots) data(trainingData) …
user321627
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Error saying I have NA/NaN/Inf value when there seems to be none present. Error in hclustfun(distc) : NA/NaN/Inf in foreign function call (arg 11)

I have a file that looks like this : Taxa,D0,D1,... 1,0,10,... 20,0,0,... ... The file is available here : https://www.dropbox.com/s/lvtxztz3kypnxre/Taxa_Conf.csv?dl=0 When I run a script by $CONCOCT/scripts/ConfPlot.R -c Taxa_Conf.csv -o…
wkde
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Axis labels not changed in gplots.plotmeans

When creating a plot using gplots.plotmeans, the axis labels are not set to what I want, but to "means" and "Index". Here is the code: library(gplots) plotmeans(ioe.dimension ~ ioe$profile, col=3, xlab="Profile", …
Ricardo Gouveia Rodrigues
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How to color labels of dendogram with dendextend and heatmap.2 using pre-defined sample groups

heatmap.2 assigns incorrect colors to labels when using "colRow" argument. Is there an alternative way how to assign colors to labels in heatmap.2? Or am I doing something wrong? (examples are based on examples from Label and color leaf dendrogram…
al-ash
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venn diagram with categorical data

I have three categorical vectors that represent symptoms. And I would like plot a venn diagram that show how many people have one two or three of them. I tryed do library(gplots) venn(list(sym1, sym2, sym3)) but didn't work Thank you sym1=c(0, 0,…
Mariane Campos
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ignore values below threshold in adjacency matrix for heatmaps in R

I have an adjacency matrix (netm) with co-occurrences as mostly 0's. I get the heatmap below when I plot it using: require(gplots) heatmap.2(netm,col=c("gold", "dark orange","orange","yellow"), Rowv=F, Colv=F, dendrogram="none", scale="none",…
EricA
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ROCR / Gplot issue

I'm trying to install the ROCR package via the following code install.packages("ROCR") install.packages("gplots") library(gplots) library(ROCR) However, I am receiving the following error: > library(gplots) Error: package or namespace load failed…
Jonas Mccloy
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Creating color breaks for each column in heatmap.2

I am trying to create a heatmap of metrics. I have used multiple questions on SO to get this far, but it seems like my solution is unique. I have 3 columns that I am tracking: OTD, TAT, and DIH. I would like to have color breaks for each of these…
Kevin
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Create annotation for a balloon plot from gplots package

I was wondering if it is possible to change the rows and columns annotation of a balloon plot generated by the gplots package. Assuming my data are a subset of the mtcars dataset data(mtcars) dt <- as.table(as.matrix(mtcars[1:10,])) I can make the…
pisistrato
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Removing white lines in colkey of a heatmap

I am trying to create a heatmap but the color key has some white lines. Questions#1: How can I remove these white lines?The range should be from -100 to 100. Only "0" should be white in the color key. Question#2: How can I remove the "X" in the…
Lyndz
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R - heatmap.2: reorder rows and columns

I generated a heatmap using heatmap.2 of the gplots package: library(gplots) abc <-read.csv(file="abc.txt", header=T, sep="\t", dec=".") abcm<-as.matrix(abc) def <-read.csv(file="def.txt", header=T, sep="\t", dec=".") defm<-as.matrix(def) mean…
rororo
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Is there a way to have a heatmap.2 axis label shared between multiple rows or columns?

I have a heatmap and want to create shared labels for multiple columns, i.e. a label for columns 1 and 2 and a label for columns 3 and 4 (or any combination of columns). Is this possible with heatmap.2? Current plot: Desired output:
Tom Nash
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