I'm working with the pheatmap package. By default, it draws the plot to the screen. In my case, that means output in a R markdown notebook in R studio. But I also want to save to a file. If I save ...

I am using pheatmap to create a heatmap of values and would like to label the legend with the units of the z values in the matrix. In this example I would like the top of the legend to say Temperat...

I have a selected group of genes I would like to plot which I have renamed. But when plotting them I also get the NAs for the non-selected. How could I remove the NAs only plotting my selected gene...

I am facing a strange problem with google heatmap. Heatmap shows less datapoints on increasing number of coordinates in heatmap data. For 333 coordinates, heatmap shows datapoints like: And for 9...

I am plotting a heatmap using pheatmap (Documentation). I am plotting a matrix in a fairly straightforward way: pheatmap(mat, annotation_col=df, labels_col=rld$Infection_Line, fontsize_row=5, font...

Using R package pheatmap to draw heatmaps. Is there a way to assign a color to NAs in the input matrix? It seems NA gets colored in white by default. E.g.: library(pheatmap) m<- matrix(c(1:100)...

How can you set the 0-point on the color scale to white in this heatmap? Does it use the breaks parameter? In the following code, white is set to 3 (or nearby on the scale): test = matrix(rnorm(2...

I am making a heatmap using the pheatmap package in R. By default the rownames are shown on the right side of the heatmap. Does anyone know how to move them to the left side? Some other packages s...

Reproducible Data: data(crabs, package = "MASS") df <- crabs[-(1:3)] set.seed(12345) df$GRP <- kmeans(df, 4)$cluster df.order <- dplyr::arrange(df, GRP) Data Description: df has 5 nume...

I was wondering if anyone knows of a package that allows partial row labeling of heatmaps. I am currently using pheatmap() to construct my heatmaps, but I can use any package that has this function...

I faced a very weird error, possibly a bug in R 3.5.1 or pheatmap The following code is working fine: rownames(df) <- colnames(mat) xx <- pheatmap(mat, annotation_col=df) But the followin...

I'm attempting to plate two plots in the same .jpg using arrangeGrob(). I've only just started learning about grids and grobs and I think I know what the problem is: pheatmap is a grid object and c...

Pheatmap library(pheatmap) takes annotation_colorsto add the header ID colors on the top of each heatmap column. I want to add white as column header color with borders. Border can be added by bo...

I know how to group rows (genes) by annotation category using pheatmap, and I know how to perform Person's correlation clustering on the whole set of rows (genes), but what I would like to accompli...

Following up on this question, I found the pheatmap function (which offers me a lot more control on the stuff that I want to do than heatmap.2). I have 2 problems though: 1- I cannot change the c...

Let's say: m1<-matrix(rnorm(1000),ncol=100) and defining colours: cols = colorRampPalette(c("white", "red"))(30) I am producing a heatmap without clustering with pheatmap function: pheatm...

The x-axis labels of heatmaps produced by package pheatmap are 270 degrees rotated by default. I need to make them 90 degrees rotated. I have traced the pheatmap() function and see there is an int...