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Question: Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
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gravatar for Kurinji Pandiyan
5.4 years ago by
Kurinji Pandiyan30 wrote:
Dear All, I am using package gplots - heatmap.2 - function to plot some data. I would really appreciate your help customizing my heatmap in terms of - 1. *adjusting color range on heatmap.2* - I am using color "greenred" and would like this to consistently range from 0-1. Because one of my datasets does not have values ranging all the way to one, the color scale has been adjusted from 0-0.5, with red being 0.5. This is confusing as it is not consistent with all the other heatmaps where red indicates a value of 1. I would like to change the range of the color scale to always be the same, regardless of dataset - always 0 being green and red being 1, with a gradation of black in between (which greenred does by default anyway) 2. *obtaining a legend for RowSideColors* - I am also trying to use a specific column of my dataframe, which has 6 different levels of annotation, to plot RowSideColors - I was able to do this: x <http: hct.delta.body.ma=""/> <- y[,c(3,9:10)] # 3 is the column with the levels of interest - for coloring - and is labeled "USCS" z <http: hct.delta.ma=""/>.ma <- as.matrix(y[,9:10]) mycol <- c("red", "green", "blue", "purple", "yellow", "black") heatmap.2z.ma <http: hct.delta.ma=""/>, col=greenred, scale = "none", trace="none",keysize = 1.5, main = list("Accessibility Plot", cex = 1.5), margins = c(5,5), cexCol = 1, Rowv = "NULL", RowSideColors=mycol[as.integer( x <http: hct.delta.body.ma=""/>$USCS)]) This worked well - only issue is, I am not sure how it picked which color to which value. I was eventually able to figure it out with a small sample set but it will be nice to not have to figure it out and to just use code to produce a legend with color and level name. Please let me know how to produce a legend with the colors used for RowSideColors. I would greatly appreciate someone's input. Thanks, Kurinji Graduate Student [[alternative HTML version deleted]]
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