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Questions tagged [pheatmap]

A package for drawing pretty heatmaps in R.

pheatmap is a package for drawing pretty heatmaps in R. The ordinary heatmap function in R has several drawbacks when it comes to producing publication quality heatmaps. It is hard to produce pictures with consistent text, cell and overall sizes and shapes. The function pheatmap() tries to alleviate the problems by offering more fine grained control over heatmap dimensions and appearance.

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Heatmap is not rendered in shiny unless I resize the window

I am new to shiny and trying to make a shiny app. I need to plot a heatmap using pheatmap based on the numeric input from user. The data is too big, but here is a reproducable data: a<-structure(list(gene_name = c("NAT2", "ACADS", "ACAT1", "ADA", …
phago29
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Pheatmap - Annotation: Subscript out of bounds error

Test RData: https://www.dropbox.com/s/hy56owg4mfjuxol/Test_Data.RData?dl=0 CSV: https://www.dropbox.com/s/hs6qpoxyg54ehid/Test_Data.csv?dl=0 Annotations: https://www.dropbox.com/s/akv66euwh3ulia2/Test_Data_Annotation?dl=0 Plotting this dataset runs…
user3012926
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Changing branch length in dendrogram (pheatmap)

I am trying to plot a heatmap with the library pheatmap in R. I think that by default the branch length is proportional to the "dissimilarity" of the clusters that got merged at this step. I would like to chance that, so it is a fixed value because…
nhaus
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how to get the column names in pheatmap in shiny?

i want to create a heatmap from user csv file in shiny, so far i have succeeded in reading the table in Shiny and also got the heatmap. however, the row names from the input csv file are not shown in the heatmap. the column names seems to appear…
Najeha Mohamed
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How to fix rows order with pheatmap?

I have generate a heatmap with pheatmap and for some reasons, I want that the rows appear in a predefined order. I see in previous posts that the solution is to set the paramater cluster_row to FALSE, and to order the matrix in the order we want,…
Vincent Darbot
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pheatmap in rstudio error" incorrect number of dimensions"

I have a large data set of genes and tissues of 3000 rows and 53 columns . when i try to create a heatmap using pheatmap in R for small number of columns it is successful. but when i try to add the annotation_col and row with color bar to heatmap, I…
Aparna Prasad
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How to get a continuous scale bar in pheatmap

I am working on microarray data and to represent the data, we chose to use heatmaps. I used pheatmap for the same. Using the code my_palette <- colorRampPalette(c("green", "black", "red"))(n = 9999) pheatmap(dts, color = my_palette, cluster_rows=T,…
vinay rao
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How to insert multiple vertical and horizontal lines in pheatmap in R?

I am trying to insert vertical and horizontal lines at desired co-ordinates inside a heatmap produced by pheatmap in R. mat <- matrix(rnorm(200*200),200,200) pheatmap(mat,treeheight_row = 0, treeheight_col = 0, col=…
StatStudent19
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expansion of an object name in R as filename to pdf function in R

I am trying to loop through bunch of files and for each file I want to make a pdf file with pheatmap function. I have written something like this: lapply(files, function(x) { a <- basename(x) a <- gsub(".txt","",a) d <-…
user3138373
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Remove NAs from dataframe generated with full_join from two scRNA-seq dataframes with equal nrow values and rownames

I've been working with a Log2 dataframe which looks like this: library(dplyr) str(df[1:10]) $ 5W_Female_C#1_1 : num 0 0 0 0 0 ... $ 5W_Female_C#1_2 : num 2.28 0 0 0 0 ... $ 5W_Female_C#1_3 : num 0 0 0 0 0 ... $ 5W_Female_C#1_4 :…
Francisco Vieira
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Pheatmap: Make hierarchical clustering on full matrix but only display subset of rows

I have a gene expression data set and want to show a heatmap of some of the genes. First, I want to make hierarchical clustering based on all genes, and create a dendrogram, and then create a heatmap on a subset of those genes. In explicit, the…
arvchi
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Pheatmap scaling creates blank lines (missing values)

I have a matrix with gene expression values, and want to plot that in a heatmap. However, when I use the scaling option, scale = "row", some blank (greyed out) lines appear in the heatmap. Because of these, pheatmap doesn't allow any clustering…
arvchi
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How to anchor color scale to the min / max for each row using pheatmap in R

I'm currently using pheatmap in R to create a heatmap of gene expressions from single cell data. The problem I am currently having is that I can't seem to replicate the relative color scale used in other heatmap generators, such as Morpheus:…
Tahoe155
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How to change plotting parameters of a function within a wrapper (R)

I'm trying to generate heatmaps by using cellrangerRkit package. The function within this package refers to pheatmap function featured in pheatmap library as seen below: gbm_pheatmap function (gbm, genes_to_plot, cells_to_plot, n_genes = 5, colour =…
Atakan
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Change colors in multiple annotations

I want to change the colors of multiple annotations of my heatmap. Example code: #test data test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3 test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] +…
Rashedul Islam
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