similar to: flip heatmap (pheatmap)

Displaying 20 results from an estimated 1000 matches similar to: "flip heatmap (pheatmap)"

2017 Sep 18
0
pheatmap: incomplete figure
> On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help <r-help at r-project.org> wrote: > > Dear R Community, > I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script: >> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA) > and got the graph (as attached Fig 1) > > Since the column labels appear very crowded, I
2017 Sep 18
2
pheatmap: incomplete figure
Dear R Community, I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script: > pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA) and got the graph (as attached Fig 1) Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with
2003 Sep 11
3
Flipping a heatmap
Hi I am using the heatmap function in package mva to look at large correlation matrices visually. Is there any way to "flip" the output of heatmap plot left-right so that, if presented with a correlation matrix, it plots the unity elements in the correlation matrix along a diagonal from top left to bottom right? For example: library(mva) x = matrix(rnorm(1000), ncol=10) z = cor(x)
2013 Dec 12
1
Heatmap, and heatmap.2 gave different figures for the same dataset
I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,
2009 Sep 12
0
consistent results with heatmap.2
Hi, I am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will
2010 Mar 07
0
How the change the dimension of an individual cell [i.e. the cell corresponding to an observation in data matrix] in a heatmap.2?
Dear R-Helpers, I have a short question related to heatmap.2 function. I wanted to change the dimension of each cell in the heatmap drawn by this function. here is a reproducible example from the help page library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x), start=0, end=.3) hv <- heatmap.2(x, col=cm.colors(255),
2011 Oct 18
0
heatmap
Dear R users, need help with my heatmap. I will really approciate some help. Given the matrix: > head(x) A B C D time [1,] 0 8 0 0 1 [2,] 0 160 0 0 2 [3,] 0 175 0 0 3 [4,] 0 253 0 0 4 [5,] 79 212 0 0 5 [6,] 6 105 0 0 6 and call: ##------------ Heatmap -------------- library(RColorBrewer) rc <- grey((nrow(x):1)/nrow(x)) heatmap(data.matrix(x[,1:4]),
2009 Apr 02
0
multiple annotations on a heatmap
Can someone recommend a more sophisticated way to annotate heatmaps than the ColSideColors argument of heatmap and heatmap.2? In particular, I would like to be able to annotate columns with more than one piece of information, like in Figure 1 of the article at http://www3.interscience.wiley.com/cgi-bin/fulltext/117905619/HTMLSTART / doi:10.1002/hep.22256. Some example data and a heatmap:
2009 Jul 23
0
using k-means clustering in conjunction with heatmap.2 function
Hello, I am trying to create a heatmap that clusters based on a k-means scheme rather than a hierarchical clustering scheme. Suppose I have the following input data, located in sample.table: x1 x2 x3 x4 x1 17.198 16.306 16.806 16.374 x2 14.554 10.866 15.780 14.596 x3 14.374 14.118 14.569 17.352 x4 17.505 14.596 15.738 14.070 By using the heatmap.2 function as follows, I can create a heatmap
2012 Jun 06
0
heatmap.2 clustering and adding add.expr
Hi , I am trying to plot a heatmap with a correlation matrix and trying to highlight significant correlations . i am using my matrix d874n has 78 columns ex2<-corAndPvalue(data.matrix(d874n),use = "pairwise.complete.obs") ##creating a matrix of true false using p values sig<-ex2$p<0.05 nx=78 ny=78 makeRects <- function(tfMat,border){ cAbove =
2005 Jul 21
0
reorder bug in heatmap.2?
I want to plot a heatmap without reordering the columns. This works fine in "heatmap": > heatmap(meanX[selected,], col=cm.colors(256), Colv=NA) But in "heatmap.2" I get: > heatmap.2(meanX[selected,], col=cm.colors(256), Colv=NA) Error in if (!is.logical(Colv) || Colv) ddc <- reorder(ddc, Colv) : missing value where TRUE/FALSE needed (Note that instructions for
2005 Aug 11
0
easier way to print heatmap on multiple pages?
Hi All, I've worked on some code to take a heatmap with 1000 row entries, and split this up into 20 pages, each with 50 rows from the original heatmap. I want to preserve the row order such that all 20 pages, if put together, would comprise the original heatmap. Here's what I've done: ##make the initial heatmap, with all 1000 rows and write it to an object 'heatAll'
2011 Apr 26
0
Questions about 'heatmap.2' function
I am trying a heatmap. I have 30 individuals and 1,000 genes. Some components I want for this heatmap plot: (1) the 'color-key'; (2) a banner across the top to emphasize how the hierarchical clustering has correctly split the data into the two groups; I use the 'heatmap.2' function in the 'gplots' package, and my function is as below:
2011 Aug 08
1
Creating a simple 1-row heatmap
Howdy, I am trying to make a simple monochrome heatmap from 1 row of data. Essentially, I just want a long bar where black represents the max value in the data, white is the minimum, and all values in between are interpolated appropriately. I have tried using heatmap and heatmap.2, but both have issues. heatmap seems to be restricted to only drawing a square plot, and this data requires a
2004 Feb 16
1
labRow/labCol options in heatmap()
The function heatmap() allows to specify row/column labels via the options labRow/labCol. From the code of heatmap(), I understand that when no labels are specified, the row/column labels (or indices) of the input matrix are taken as labels and re-ordered together with the rows and columns of the matrix before plotting, whereas labels supplied via labRow/labCol are plotted in the original order.
2009 Jul 02
0
using heatmap.2 without specifying Colv and Rowv
Hi all, I am a novice user of the heatmap.2 function in the Bioconductor gplots package. I am trying to create a heatmap diagram from a hierarchical clustering result based on the complete linkage and the pearson correlations as the distance metrics. After reading the help page for heatmap.2, it seems that it calls the distfun and hclustfun with the default settings. Is that the same as doing
2004 Aug 25
1
Problems with Heatmap
Hi I am having some problems getting my heatmap to be the right size! Let me explain. I am experienced at getting an hclust or a dendrogram object to be the right size. For example, I have a dataset which has 4000 rows, which I clustered using hclust and I wanted to plot it as a horizontal dendrogram. So I used jpeg(), set the image height to be 4000 and plotted the dendrogram and got the
2004 Dec 15
1
hclust and heatmap - slightly different dendrograms?
Good afternoon, I ran heatmap and hclust on the same matrix x (strictly, I ran heatmap(x), and hclust(dist(t(x))), and realized that the two dendrograms were slightly different, in that the left-right arrangement of one pair of subclusters (columns) was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite
2010 Feb 10
2
color palette heatmap
Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them
2009 Jan 20
1
heatmap.2 color issue
Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or