Re: Generating heat map of pre-organised data in matrix without clustering using ggplot2 or heatmap.2

Hi Jakub,

This discussion is getting a bit extended, particularly given that gplots
is a CRAN package, not Bioconductor. I would recommend taking these
questions to R-help, and make sure you cc the maintainer of gplots.

Best,

Jim




On Sat, Aug 9, 2014 at 11:40 PM, Jakub Stanislaw Nowak <[email protected]
> wrote:

> Hi James,
>
> Many thanks for your email. I managed to make the heat map look better.
>
> However I still have some minor problems with a layout.
>
> I decided to put key above the heat map by using lmat parameter.
>
> However when I do that key is not aligned with the heat map. I believe it
> is due the mar settings for the key. Also the key.ylab overlaps with ylab
> ticks.
> I tried to call key.par setting as I think I can sort it with mar and mgp
> setting. However whenever I call key.par my key completely disappears.
> Even when I call default parameters for mar and mgp.
>
> Here is the code I used, commented out is the key.par line.
> ```{r}
> if (!require("gplots")) {
>  install.packages("gplots", dependencies = TRUE)
>  library(gplots)
>  }
> if (!require("RColorBrewer")) {
>  install.packages("RColorBrewer", dependencies = TRUE)
>  library(RColorBrewer)
>  }
> mypalette <- colorRampPalette(c("red", "black", "green"))(n = 299)
> colbreaks <- c(seq(-6,-3,length=130), # for red
> seq(-3,3,length=70), # for black
> seq(3.10,length=100)) # for green
> pdf("heatmap.pdf",10,15),
> heatmap.2(data.heatmap.matrix,
>   Colv="FALSE",
>   Rowv="FALSE",
>   main = "Corelation",
>   notecol="black",
>   density.info="density",
>   trace="none",
>   colsep=1,rowsep=c(1:51),sepcolor="grey",sepwidth=c(0.005,0.01),
>   labCol=c("lineA","LineB"),
>   srtCol=0,
>   cexCol = 1.5,
>   offsetCol=(4),
>   adjCol=c(0.48,0),
>   margins =c(5,8),
>   col=mypalette,
>   breaks=colbreaks,
>   keysize=0.1,
>   #key.par=list(mar=c(2, 2, 2, 1), mgp=(2,1,0)),
>   key.title=NA,
>   key.xlab=("Fold change"),
>   key.ylab=("Density"),
>   key.xtickfun=function(){
>     key.breaks <- parent.frame()$breaks
>     return(list(
>
> at=parent.frame()$scale01(c(key.breaks[1],key.breaks[length(key.breaks)])),
>
> labels=c(as.character(key.breaks[1]),as.character(key.breaks[length(key.breaks)]))
>       ))
>         },
>   symkey=FALSE,
>   lmat=rbind( c(3), c(0,4), c(2,1)), lwid=c(1.5,4), lhei=c(0.25,1,4),
>   )
> dev.off()
>
> ```
>
> I would be grateful if some solution can be suggested,
>
>
>
> Thanks,
>
> Jakub
>
>
> On 8 Aug 2014, at 16:17, James W. MacDonald <[email protected]> wrote:
>
> Hi Jakub,
>
> On Fri, Aug 8, 2014 at 7:06 AM, Jakub Stanislaw Nowak <
> [email protected]> wrote:
>
>> Hello bioconductor friends,
>>
>> I am trying to generate heatmaps for my data and run in following
>> problems. I would be grateful for some suggestions about heat map code.
>>
>> I arranged matrix for the heatmap by myself and I would like to keep this
>> not changed during heat map plotting. I tried both heatmap.2 (gplot) and
>> geom_tile (ggplot2)
>>
>> 1. So when I used heatmap.2 from (gpot) it keeps my matrix sort but I
>> have problems making the layout look nice. Below is the code I used.
>> Can you suggest how to:
>> a) make rows and columns separated and rows bigger so it can read easier.
>>
>
> Put it in a pdf that is longer than it is tall:
>
> pdf("heatmap.pdf', 10,50)
> heatmap.2(<args>)
> dev.off()
>
>
>> b) is there a way for changing  x label for key so it includes min and
>> max values for colour code.
>>
>
> Well you can change the x label, but I don't think that is what you are
> talking about. Instead I believe you are asking about the x tick labels. In
> which case, from ?heatmap.2:
>
> key.xtickfun: function computing tick location and labels for the xaxis
>           of the color key. Returns a named list containing parameters
>           that can be passed to ‘axis’. See examples.
>
> And as advertised, there is an example of how you can change things.
>
> c) can the density plot be generated above the key
>>
>
> Of course! Anything _can_ be done. But that doesn't mean it will be easy
> to do. Right above the example that shows how to change the key axis labels
> is an example of how you can use the 'extrafun' argument to replace the key
> entirely with a scatterplot. You could write a function that generates the
> key with a density plot right above it, and then pass that in via the
> extrafun argument.
>
> Best,
>
> Jim
>
>
>
>>
>> Preparing table for the heatmap.2 from (qplot)
>> ---------------------------------------
>> ```{r}
>> data.heatmap <- data.sorted.merged[,-c(2:5,8),drop=FALSE]
>> rownames(data.heatmap)<-data.heatmap$ID
>> data.heatmap <- data.heatmap[,-1]
>> data.heatmap.matrix <- data.matrix(data.heatmap)
>> ```
>> Generating heatmap with heatmap.2
>> ------------------------------
>> ```{r}
>> if (!require("gplots")) {
>>  install.packages("gplots", dependencies = TRUE)
>>  library(gplots)
>>  }
>> if (!require("RColorBrewer")) {
>>  install.packages("RColorBrewer", dependencies = TRUE)
>>  library(RColorBrewer)
>>  }
>> mypalette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)
>> #subseting default gradient with custom one for better visualisation
>> colbreaks <- c(seq(-6,-3,length=110), # for red
>> seq(-3,3,length=90), # for yellow
>> seq(3.10,length=100)) # for green
>> heatmap.2(data.heatmap.matrix,
>>   main = "Correlation", # heat map title
>>   notecol="black",      # change font color of cell labels to black
>>   density.info="density",  # turns density plot inside color legend
>>   trace="none",# turns off trace lines inside the heat map
>>   scale=c("none"),
>>   colsep, rowsep, sepcolor="white", sepwidth=c(1,1), #doesn't really
>> show any separation
>>   margins =c(1,15),     # widens margins around plot doesn't do much
>>   col=mypalette,       # use on color palette defined earlier
>>   breaks=colbreaks,    # enable color transition at specified limits
>>   Rowv="NA",     # only draw a row dendrogram
>>   Colv="NA",    # turn off column clustering
>>   key.title=NA, # no title
>>   symkey=FALSE,
>>
>>   )
>> ```
>>
>> 2. I also tried to use geom_tile from (ggplot2) to generate this heat
>> map. Here layout looks better but I am loosing my organisation of the
>> matrix. Below is a code I used to make a plot
>> Can you suggest:
>> 1. how to switch off clustering in ggplot2
>>
>> Generating heatmap with ggplot2
>>
>> ```{r}
>> if (!require("reshape2")) {
>>  install.packages("reshape2", dependencies = TRUE)
>>  library(reshape2)
>>  }
>> if (!require("plyr")) {
>>  install.packages("plyr", dependencies = TRUE)
>>  library(plyr)
>>  }
>> if (!require("scales")) {
>>  install.packages("scales", dependencies = TRUE)
>>  library(scales)
>>  }
>> if (!require("ggplot2")) {
>>  install.packages("ggplot2", dependencies = TRUE)
>>  library(ggplot2)
>>  }
>> data.sorted.merged.test <- data.sorted.merged[,-c(2:5,8)]
>> data.heatmap2 <- melt(data.sorted.merged.test)
>> data.heatmap2 <- ddply(data.heatmap2, .(variable), transform,rescale =
>> rescale(value))
>> ggplot(data.heatmap2, aes(variable, ID))+ geom_tile(aes(fill=rescale),
>> colour="white") +
>>   scale_fill_gradient(low="white", high="red", breaks=colbreaks)
>> ```
>>
>> Also I can attach png files of the heat map if that can help.
>>
>> Thanks very much for your help,
>>
>> Jakub
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>


-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor