pheatmap

问题 I am using the R heatmaply package to produce interactive heatmaps. I like the software, but I would like to get from it the same color output I get using the pheatmap package. Therefore, I would like the two commands to produce the same ouput: heatmaply (scale (mtcars)) pheatmap (scale (mtcars)) Is there a way to do this? Thanks in advance. Arturo 回答1: You can use formals() to get the default color argument of pheatmap() . formals(pheatmap)$color # colorRampPalette(rev(brewer.pal(n = 7, name

问题 I am using the R heatmaply package to produce interactive heatmaps. I like the software, but I would like to get from it the same color output I get using the pheatmap package. Therefore, I would like the two commands to produce the same ouput: heatmaply (scale (mtcars)) pheatmap (scale (mtcars)) Is there a way to do this? Thanks in advance. Arturo 回答1: You can use formals() to get the default color argument of pheatmap() . formals(pheatmap)$color # colorRampPalette(rev(brewer.pal(n = 7, name

问题 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(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)] + 2 test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4 colnames(test) = paste("Test", 1:10, sep = "") rownames(test) = paste("Name", 1:20, sep = "") pheatmap(test,

问题 I would like to make an heatmap in R using pheatmap with the colors green, black and red and using a range in the legend from -2 to 2, here is the code that I used: library(pheatmap) my_palette <- colorRampPalette(c("green", "black", "red"))(n = 201) colors = c(seq(as.numeric(-2),-0.01,length=100), 0, seq(0.01,as.numeric(2),length=100)) pheatmap(mFilt_annot_sort_matrix, color = my_palette, breaks = colors, scale = "none", cluster_rows = F, cluster_cols = F, margin = c(5,5)) The problem is

问题 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, fontsize_col=7) The bottom of my plot is getting cut off so that I can't see the column names at the bottom. It looks like this: Please note that this is not heatmap.2. I have tried the solutions at this question and at this question, as well as other things I've been able to find through google and in

问题 I have a data frame of items, and each has multiple classifier columns that are categorical variables. ID test1 test2 test3 1 A B A 2 B A C 3 C C C 4 A A B 5 B B B 6 B A C I want to generate a heatmap for each combination of test columns (test1 v test2, test1 v test3, etc.) using ggplot2. The heatmap would have all factors in that test's column (in this case A,B,C) on the x-side and all factors of the other test on the y-side, and the boxes in the heatmap should be colored based on the count

问题 I have used single cell RNA-seq data stored in a single cell experiment assay to perform hierarchical clustering of ~ 11.3000 expressed genes (not clustering samples) using pheatmap in R to show the heterogeneity of the data. I need the output image to be 2 x 4 inches, which makes the dendrogram a blur. Is it possible to reduce the line width used for the dendrogram? I tried setting the line width by gpar, but it doesn't seem to change sessionInfo() R version 3.4.1 (2017-06-30) Platform: i386

问题 I am very new to R and recently I have been playing around with the pheatmap library to generate, well, heatmaps. My problem is that I want to color my heatmap in a specific way. I'll describe below: Values < 1 should be a color ramp (e.g. dark blue to light blue) A value exactly equal to 1 should be dark grey Values > 1 should be a color ramp (e.g. dark red to light red) I have played around with the breaks parameter and the color parameter with various palettes but I can't seem to nail a

问题 I wish to create something similar to the following types of discontinuous heat map in R: My data is arranged as follows: k_e percent time .. .. .. .. .. .. I wish k_e to be x-axis, percent on y-axis and time to denote the color. All links I could find plotted a continuous matrix http://www.r-bloggers.com/ggheat-a-ggplot2-style-heatmap-function/ or interpolated. But I wish neither of the aforementioned, I want to plot discontinuous heatmap as in the images above. 回答1: The second one is a

问题 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 numerical variables. I did the K-means algorithm according to these 5 attributes and produced a new categorical variable GRP which has 4 levels. Next, I ordered it with GRP and named it df.order . What I did with pheatmap : ## 5 numerical variables for coloring colormat <- df.order[c("FL", "RW", "CL", "CW", "BD")] #