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Question: Adding a text label to the classvec colour bar in heatplot
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gravatar for Amy Mikhail
9.3 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Dear BioCs, I'm trying to create a heat plot with a matrix containing real time PCR data for just 5 genes. There are 105 samples, belonging to 7 groups (groups are in numerical order). The matrix looks like this (Age is my grouping variable): Gene1 Gene2 Gene3 Gene4 Gene5 Age A1R_D03 -13.71434 -14.19288 -15.79439 -14.93712 -14.87174 3 A4R_D03 -13.29068 -13.39888 -16.49077 -14.87276 -15.21852 3 A7R_D03 -13.19423 -13.09508 -15.80787 -14.59671 -14.47190 3 A10R_D03 -13.33472 -13.34051 -15.60396 -14.69521 -14.28135 3 A13R_D03 -11.89260 -11.73026 -16.05069 -14.59895 -16.40680 3 A61K_D03 -14.64341 -14.55358 -16.37900 -15.44644 -15.80778 3 ...etc As there are so many samples, it doesn't make sense to have the individual sample names on the graph, so I would like to have the samples in their group order with just the seven group labels. With heatplot I can get the colourbar for my seven groups using the classvec argument, but can't find any way to label the colourbars with text... Also, I'm a little confused about the re-ordering that heatplot does - how can I be sure that the samples belonging to a particular group are underneath the appropriate colourbar (and given my situation I would also want the groups to appear in numerical order)? I have tried using heatmap.2 as well, but it seems only heatplot has the colour bar by group option - heatmap.2 only allows you to add a colourbar representing each column separately? Here is my code: #(Ngenet is a transposition of my matrix and the Age variable is in a separate dataframe so that it doesn't appear directly on the plot). >heatplot(Ngenet, dend="none", cols.default=FALSE, margin=c(7, 7), labCol=FALSE, lowcol="red", highcol="green", scale="none", classvec=Mop$Age) If anyone could suggest how I might add the group labels, I'd be very grateful - appologies if this is something very simple, I have actually seen papers with plots showing exactly what I want to do but just can't figure out how to do it. With best wishes, Amy ---------------------------------------------------------------------- -------------- Amy Mikhail Research student Parasite and Vector Biology group University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-273256 (office) The University of Aberdeen is a charity registered in Scotland, No SC013683.
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