similar to: question about function heatmap

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

I would like to draw horizontal or vertical lines on a heatmap to highlight the clusters at some specified cut depth of the dendrogram. As a hacked example, the following code would work if I could set the coordinates of the top and bottom of the false color image correctly (ymin and ymax), but the correct values seem to depend on the output device and its size. I realize that heatmaps use a 2x2

Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried >heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hi, In perl, to get a substring matching a particular pattern can be implemented like the following example: $x = "AAAA.txt"; if ($x=~ /(.*?)\.txt/){ $prefix = $1; } So how to do the same thing in R? Can someone provide me the code sample? Thanks much in advance. -- Waverley @ Palo Alto

Hi, Can someone help as how to use R to program google search in the R code? I know that other languages can allow or have the google search API If someone can give me some links or sample code I would greatly appreciate. Thanks. -- Waverley @ Palo Alto

I use ROCR to plot multiple runs' performance. Using the sample code as example: # plot ROC curves for several cross-validation runs (dotted # in grey), overlaid by the vertical average curve and boxplots # showing the vertical spread around the average. data(ROCR.xval) pred <- prediction(ROCR.xval$predictions, ROCR.xval$labels) perf <- performance(pred,"tpr","fpr")

Dear Colleagues, I am looking for a package or previous implemented R to subgroup and exaustively divide a vector of squence into 2 groups. For example: 1, 2, 3, 4 I want to have a group of 1, (2,3,4) (1,2), (3,4) (1,3), (2,4) (1,4), (2,3) (1,2,3), 4 (2,3), (1,4) ... Can someone help me as how to implement this? I get some imaginary problem when the sequence becomes large. Thanks much in

Hi, I tried to use boxplot function. I am following the ?boxplot and can change the whisker box width using lwd parameter. However, when outline=TRUE, the thickness of the circle of the outliers is not proportionally changed when I change the line width of the whisker box. There must be another parameter for that. Unfortunately I don't know. please help and thanks much in advance. --

Hi, I have a question of aov. e.g. aov.ex = aov(x~y) summary(aov.ex) The aov summary will print to the screen. How can I extract the aov result, in particular the values of Pr(>F) and F value into a vector so that I can use them for other use? Thanks. -- Waverley @ Palo Alto

Hi, I have a matrix a = matrix (1:16, 4, 4) b = c (2,3) I want to find out which rows of a, where a[,1] equals any values of b? I know that if b is only one value, e.g, b=2, then what I want is a[a[,1] == 2,] But what about if it is not one value but a vector of values? Thanks much in advance. -- Waverley @ Palo Alto

Hi, I have a question about ROCR package. I got the ROC curve plotted without any problem following the manual. However, I don't know to extract the values, e.g. y.values ( I think it is the area under the curve auc measure). The return is an object of class "performance" which have Slots and one of the slot is "y.values". I type the object and I can see them in

Hello, I've been clustering my data using hclust and cutting the resulting tree with cutree. Separately, I visualize the clusterings with heatmap. Is it possible to have the dendrogram on the heatmap reflect the cutree results? That is, instead of having one large dendrogram, it would have 4 or 25 in the example below. Any guidance on if that's possible or not, and what kinds of

Hi, I am thinking about using R to create a database, then create table in MySQL server. Can I do that using RMySQL package? I am familiar with RMySQL, and in the online help most of the sample code assumes the database exists and transact with the table inside the database. Can someone provide me some sample code to create a database and table? Specifically create a database first, then

hi, i have a data frame like this: 0.3 0.7 0.4 0.8 i am trying to plot this data frame and each cell is filled with different colors based on the value. Is there a function which can do this? thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi, I understand for 1 d classifiers, you can use ROCR package. Is there a package you can plot ROC curve for 2d classifiers? One of my colleagues asked me about this. I have been quite puzzled, conceptually, how you can do the ROC curve for 2d classifiers. Can someone share his/her knowledge or experience? Thanks in advance. -- Waverley @ Palo Alto

Hi Sorry if this is in the help :-S I've looked at example(dendrogram) and though it gives some indication of what I want, it doesn't do all. OK, so here is what I want to do: draw a tree, and then have an action, on user-click, to either draw a sub tree or a plot of the data. I also want users to be able to search for a particular label and have it highlighted on the tree, say in

Hi, I want to extract some of the substring via pattern recognition. But I don't know how to do it in R. In perl: my $url = "/pages-cell.net/deepan/sony/"; if($url =~ m/\/(.*)\//g) { my @result = $1; return @result; } How does the same work in R? Thanks much in advance -- Waverley @ Palo Alto

Dear colleague, I have two data frame which I tried to use dbWriteTable function with append=TRUE to write to the mysql database. The problem is that if I am run my R script directly then it is fine. Both data frame got written into the database. But when I tried to embed the script to be called as system("R --save < whatever.R") in my perl script, I saw very strange things. One

Hello R-Helpers, I have a question about extracting the clusters of genes after we make the heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the clusters which are shown as row dendrogram in the heatmap. I understand that ht4$rowDendrogram is an object of dendrogram and it containes details of all the nodes and branches, but lets say I want to know the number of clusters