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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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Heatmap.2 Rowv=F not working to avoid reordering

I have a given matrix with a given order "filtered2" I am using from gplots to construct a heatmap that should have the same order of rows found in the matrix, however it is still reordering even using Rowv=FALSE, this is the command that I am using…
user2733850
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How to create a Venn Diagram using R?

I created a Venn Diagram using the eulerr package but it doesn't let me customize it and the outlines of the inner circles seem to touch the sample space circle. I looked through the VennDiagram package manual but had no luck. Is there a way to…
had01
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gplots heatmap.2 slow with Rowv=FALSE

I have a problem with the heatmap.2 function from gplots (version 3.0.1.1): it processes extremely slowly when both row and column clusterings are set to FALSE. Sample matrix: x <- matrix(rnorm(25000), ncol=2) With both clusterings: heatmap.2(x,…
sargg
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How to plot LTP vs. time from data available in a matrix in the form of Date, time, LTP

I have data in 3 columns:(as shown below Date Time LTP 20180102 09:16 1800 ... ... ... I wanna plot it in R so that I get time on the x-axis and LTP on the y-axis. Since there are around 360 rows every day (every…
krishna
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How to make heatmap with one column of csv data

I need to make a heatmap with only one column of data, I get error message saying "'x' must have at least 2 rows and 2 columns". How can I make heatmap in R with just one column of data? This is my code: `library(gplots) getwd() x <-…
Lydia Blakley
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cosinor2 package R error column 'Y' must be a 1d atomic vector or a list

I have been using cosinor2 for my summer project and the scripts have been working fine without any issues. But when i transfer the files to my supervisors pc and try to run the package everything works other than for the graphs that gets produced…
localpora
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R heatmap.2: How do I adjust ylim of the histogram on the color key?

For reasons of comparison of two heatmaps associating categorical variables, I would like to know how I can adjust the "Count" axis of the density plot/histogram superimposed on the color key such that in both heatmaps the keys including the…
Mario
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R: read.table for heatplot

I have the following matrix: row genome1 genome2 genome3 genome1 100 99.99 98.88 genome2 99.99 100 NA genome3 98.88 NA 100 which I want to plot as a heatmap. With the code posted below, I have problems reading the file - the rownames and header are…
rororo
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ggplot2 how to facet individual graphs across 2 pages

I have this code g=ggplot(a, aes(x = TIME, y = DV,group = ID)) g + geom_point(data = a, colour="red", size=2) + theme_bw() + geom_smooth(method = 'loess', se = FALSE,colour="black") + facet_wrap( ~ ID, ncol = 4,nrow = 6, scales =…
Muhammad Faisal
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Box plot with outliers for all variables with percentile in R

In my dataset comp=structure(list(MYCT = c(125L, 29L, 29L, 29L, 29L, 26L, 23L, 23L, 23L, 23L, 400L, 400L), MMIN = c(256L, 8000L, 8000L, 8000L, 8000L, 8000L, 16000L, 16000L, 16000L, 32000L, 1000L, 512L), MMAX = c(6000L, 32000L, 32000L, 32000L,…
psysky
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create a function that generate plots from a data

I have a data with 8 variables (x1,y1,x2,y2,x3,y3,x4,y4), and i should do a function that generate a 4 plots x1vsy1, x2vsy2, x3vsy3 and x4vsy4. So i was trying to do that one by one, doing a new data with the variables and after generate de…
fran
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Generating a Heatmap From Data Range in R

I have generated a list (named "trans") of dataframes in R. Each list has 3 columns: slope, start, and stop. Here is a small portion of the data: > trans $a slope start stop 1 0.0006718865 -0.85576923 -1.0000000 2…
BioBaker
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R: Row scaling not working correctly for heatmap

I am currently creating a heatmap for some data where the values for each item (OTU) vary greatly, so I am using the scale="row" option. I assumed that this would utilise the same colour gradient for each row so the maximum colour would always be…
thh32
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Use customized order of axis with heatmap.2 function from gplots

I need to plot a heatmap using axis ordered as is in table. My data is is csv format: "X" "Mescla" "HCL" "HSL" "Kmeans" "soma" "1" "DR" 15.33559 14.7499 14.7556 14.32343 89.78054 "2" "DA" 16.59264 14.764 14.9968 14.36513 91.08672 "3" "UMR80"…
Marc Kees
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ggplot How to display a raster without the NA values after a cut with "mask"?

After cutting my raster according to a polygon using the "mask" function : ras <- mask(ras0, polygon) I want to present the raster (link below) with ggplot. However, I have a problem with the "NA" values that located in outside of my cut…
tazrart
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