How to make a heat map with dendrogram by averaging the replicate data by tydr?

I have a dataset of >100 different samples. Samples are from different genotypes (e.g. X, Y, Z) and 4 different time points (T0,1,2,3) with 3 biological replicates (R1,2,3). I'm measuring values for 50 different genes (in raws)

   structure(list(Gene = structure(1:2, .Label = c("A", "B"), class = "factor"), X_T0_R1 = c(1.46559502, 0.220140568), X_T0_R2 = c(1.087642983, 0.237500819), X_T0_R3 = c(1.424945196, 0.21066267), X_T1_R1 = c(1.289943948, 0.207778662), X_T1_R2 = c(1.376535013, 0.488774258), X_T1_R3 = c(1.833390311, 0.182798731), X_T2_R1 = c(1.450753714, 0.247576125), X_T2_R2 = c(1.3094609, 0.390028842), X_T2_R3 = c(0.5953716, 1.007079177), X_T3_R1 = c(0.7906009, 0.730242116), X_T3_R2 = c(1.215333041, 1.012914813), X_T3_R3 = c(1.069312467, 0.780421013), Y_T0_R1 = c(0.053317766, 3.316414959), Y_T0_R2 = c(0.506623748, 3.599442788), Y_T0_R3 = c(0.713670106, 2.516735845), Y_T1_R1 = c(0.740998252, 1.444496448), Y_T1_R2 = c(0.648231834, 0.097957459), Y_T1_R3 = c(0.780499252, 0.187840968), Y_T2_R1 = c(0.35344654, 1.190274584), Y_T2_R2 = c(0.220223951, 1.367784148), Y_T2_R3 = c(0.432856978, 1.403057729), Y_T3_R1 = c(0.234963735, 1.232129062), Y_T3_R2 = c(0.353770497, 0.885122768), Y_T3_R3 = c(0.396091395, 1.333921747), Z_T0_R1 = c(0.398000559, 1.286528398), Z_T0_R2 = c(0.384759325, 1.122251177), Z_T0_R3 = c(1.582230097, 0.697419716), Z_T1_R1 = c(1.136843842, 0.804552001), Z_T1_R2 = c(1.275683837, 1.227821594), Z_T1_R3 = c(0.963349308, 0.968589683), Z_T2_R1 = c(3.765036263, 0.477443352), Z_T2_R2 = c(1.901023385, 0.832736132), Z_T2_R3 = c(1.407713024, 0.911920317), Z_T3_R1 = c(0.988333629, 1.095130142), Z_T3_R2 = c(0.618606729, 0.497458337), Z_T3_R3 = c(0.429823986, 0.471389536)), .Names = c("Gene", "X_T0_R1", "X_T0_R2", "X_T0_R3", "X_T1_R1", "X_T1_R2", "X_T1_R3", "X_T2_R1", "X_T2_R2", "X_T2_R3", "X_T3_R1", "X_T3_R2", "X_T3_R3", "Y_T0_R1", "Y_T0_R2", "Y_T0_R3", "Y_T1_R1", "Y_T1_R2", "Y_T1_R3", "Y_T2_R1", "Y_T2_R2", "Y_T2_R3", "Y_T3_R1", "Y_T3_R2", "Y_T3_R3", "Z_T0_R1", "Z_T0_R2", "Z_T0_R3", "Z_T1_R1", "Z_T1_R2", "Z_T1_R3", "Z_T2_R1", "Z_T2_R2", "Z_T2_R3", "Z_T3_R1", "Z_T3_R2", "Z_T3_R3"), class = "data.frame", row.names = c(NA, -2L))

I want to average reach 3 replicates (R1,2,3) for each time point (T0,1,3,5) and make a new matrix and then create a heat map with dendrogram.

How can I average each 3 replicates of each genotype at particular time point and make the new matrix? is this possible with tydr?

• 3,449 views • link

updated 8.1 years ago by cpad0112

• written 8.3 years ago by WUSCHEL

It's possible in tidyr/ggplot but it's awful. Just convert your data to a matrix and use heatmap.2 or complexHeatmap. I wouldn't normally average my replicates before making a heatmap though.

• 1 views • link

written 8.3 years ago by russhh

If you do not mind, could you please explain this up to the matrix, I know how to follow the rest

• 1 views • link

written 8.3 years ago by WUSCHEL

@OP: you may want to furnish example data and expected output.

• 1 views • link

written 8.3 years ago by cpad0112

Create a matrix with a row for each feature and a column for each sample, and put the values from your dataframe into the matrix. Then call [Heatmap][1]() or [heatmap][2].2 on the matrix. You can make the heatmap tiling in ggplot2 using geom_tile, but it's very difficult to overlay a dendrogram above such an image so you're better using Heatmap or heatmap.2

• 0 views • link

written 8.3 years ago by russhh

1 answer

since no one has replied, following is the answer gene vs time heatmap. Data frame (df) is constructed from OP data and replicates are average (mean).

library(tidyr)
library(dplyr)
library(ggplot2)

df2=gather(df,k,expression,-Gene) %>%
    separate(k,c("sample","time","replicate"))%>%
    group_by(Gene,sample,time) %>%
    summarise(mean=mean(expression))

ggplot(data=df2,aes(time, Gene, fill=mean)) +
    geom_tile()+
    scale_fill_gradient(low = "green", high = "red")

• 1 views • link

written 8.1 years ago by cpad0112

Thank you very much cpad0112.

• 1 views • link

written 8.1 years ago by WUSCHEL