Heatmap of diferent conditions

Question

[Leandro de Mattos]

Dear, How can I make a heatmap of these data (Table)?

Sample Conditions GrowthX GrowthY GrowthZ GrowthW 2ugAg+ Metal -3.085.361 15.085.361 -15.085.361 15.785.361 2ugAg+ Metal -3.005.842 13.005.842 -13.005.842 13.705.842 2ugAg+ Metal -2.997.751 11.996.551 -11.996.551 11.796.551 1ugZn+ Metal -2.890.344 11.340.344 -11.340.344 11.740.344 1ugZn+ Metal -2.849.076 13.459.076 -13.459.076 13759076 1ugZn+ Metal -2.809.053 11.409.053 -11.409.053 1.709.053 Ampicilin10ug Antibiotics -11.809.053 11.809.053 -11.809.053 11.709.053 Ampicilin10ug Antibiotics -10.809.053 16.769.053 -16.769.053 16.969.053 Ampicilin20ug Antibiotics -6.809.053 15.781.053 -15.781.053 15.981.053 Ampicilin20ug Antibiotics -3.809.053 11673153 -11.673.153 11.973.153

Any suggestion is welcome Thanks. Leandro

[ahmad.iut]

pheatmap package is one of the best. it will draw heatmap the same as the heatmap in the paper.

[Leandro de Mattos]

For example, in R:

x <- read.table("fitness.csv",sep=",", fill = TRUE)
x_matrix<-data.matrix(x)
row.names(x)

x_heatmap <-heatmap(x_matrix,col = cm.colors(256), scale="column")

But is not ok yet;

[Jean-Karim Heriche]

To get row and column labels, use the labRow and labCol options of heatmap(). For more complicated layouts, you should probably use one of the many alternatives e.g. heatmap.2, heatmap.3, heatmap.plus or aheatmap. You may find this post useful.

Answer 1

[Leandro de Mattos]

Dear, I managed to do the figure, sharing :

data <- read.csv2(file="result.csv", sep=";", dec=";") data rnames data[,1] rnames data <- read.csv2(file="result.csv", sep=";", dec=",") data mat_data <- data.matrix(data[,2:ncol(data)]) mat_data rownames(mat_data) <- rnames my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299) col_breaks = c(seq(-1,0,length=100), seq(0,5,length=100), seq(5,15,length=100)) heatmap.2(mat_data, cellnote = mat_data, main = "results", notecol="black", density.info="none", key.xlab="valor" trace="none", margins =c(12,9), col=my_palette, dendrogram="row",Colv="NA")

Leandro.