Error adding annotation colours to pheatmap in R: “more elements supplied than there are to replace”
I am a relative R newbie and am having some issues trying to change the colour palette used for annotations in pheatmap.
I have created an annotated heatmap from the file Total_depth_avg_mag.txt using the following commands:
library(vegan)
library(gplots)
library(dplyr)
library('pheatmap')
library(RColorBrewer)
#Reads data into table, adds row names and deletes the first column
dat<-read.table("Total_depth_avg_mag.txt", header = T)
row.names(dat) <- dat$mag
dat <- dat[, -1]
# Produces annotation data_frame from input file
data_annot_2 <- read.table("Mag_annot_taxonomy.txt", header = T)
rownames(data_annot_2) = data_annot_2$mag
data_annot <- data_annot_2["Taxonomy"]
#Produces annotated heatmap
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax.png", width =20,
height =30, border_color= NA, annotation_row = data_annot)
Which produces the following:
Heatmap_with_generic_colours
As there are quite a few (34) variables in my annotations some of them end up having the same colours so I would like to use my own palette. I used the following code to try to do this:
#Making a version of the "Greys" set from Rcolorbrewer containing 17 colours
coul = brewer.pal(9, "Greys")
coul = colorRampPalette(coul)(17)
#Producing a palette to feed into pheatmap. Contains 34 colours.
my_palette <- c(brewer.pal(9, "Reds")[c(6)], brewer.pal(9, "Greens")
[c(4,7)], brewer.pal(9, "Oranges")[c(4)], brewer.pal(9, "Blues")[c(3,5,7)],
brewer.pal(8, "Accent")[c(4)], brewer.pal(8, "Accent")[c(6)], brewer.pal(8,
"Accent")[c(7)], coul, brewer.pal(9, "Purples")[c(3,4,5,7)], brewer.pal(9,
"BuGn")[c(3,4)], brewer.pal(8, "Pastel2")[c(7)])
#Producing annotated heatmap with my_palette
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax_col.png", width =20,
height =30, border_color= NA, annotation_row = data_annot,
annotation_colors = my_palette)
I then get the error "Error in annotation_colors[[names(annotation)[i]]] <- factor_colors[ind] : more elements supplied than there are to replace"
I'm not sure why this is as my_palette definitely has 34 colours in it and my annotation should contain 34 variables.
Can anyone suggest anything to fix this?
r pheatmap
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
add a comment |
I am a relative R newbie and am having some issues trying to change the colour palette used for annotations in pheatmap.
I have created an annotated heatmap from the file Total_depth_avg_mag.txt using the following commands:
library(vegan)
library(gplots)
library(dplyr)
library('pheatmap')
library(RColorBrewer)
#Reads data into table, adds row names and deletes the first column
dat<-read.table("Total_depth_avg_mag.txt", header = T)
row.names(dat) <- dat$mag
dat <- dat[, -1]
# Produces annotation data_frame from input file
data_annot_2 <- read.table("Mag_annot_taxonomy.txt", header = T)
rownames(data_annot_2) = data_annot_2$mag
data_annot <- data_annot_2["Taxonomy"]
#Produces annotated heatmap
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax.png", width =20,
height =30, border_color= NA, annotation_row = data_annot)
Which produces the following:
Heatmap_with_generic_colours
As there are quite a few (34) variables in my annotations some of them end up having the same colours so I would like to use my own palette. I used the following code to try to do this:
#Making a version of the "Greys" set from Rcolorbrewer containing 17 colours
coul = brewer.pal(9, "Greys")
coul = colorRampPalette(coul)(17)
#Producing a palette to feed into pheatmap. Contains 34 colours.
my_palette <- c(brewer.pal(9, "Reds")[c(6)], brewer.pal(9, "Greens")
[c(4,7)], brewer.pal(9, "Oranges")[c(4)], brewer.pal(9, "Blues")[c(3,5,7)],
brewer.pal(8, "Accent")[c(4)], brewer.pal(8, "Accent")[c(6)], brewer.pal(8,
"Accent")[c(7)], coul, brewer.pal(9, "Purples")[c(3,4,5,7)], brewer.pal(9,
"BuGn")[c(3,4)], brewer.pal(8, "Pastel2")[c(7)])
#Producing annotated heatmap with my_palette
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax_col.png", width =20,
height =30, border_color= NA, annotation_row = data_annot,
annotation_colors = my_palette)
I then get the error "Error in annotation_colors[[names(annotation)[i]]] <- factor_colors[ind] : more elements supplied than there are to replace"
I'm not sure why this is as my_palette definitely has 34 colours in it and my annotation should contain 34 variables.
Can anyone suggest anything to fix this?
r pheatmap
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
add a comment |
I am a relative R newbie and am having some issues trying to change the colour palette used for annotations in pheatmap.
I have created an annotated heatmap from the file Total_depth_avg_mag.txt using the following commands:
library(vegan)
library(gplots)
library(dplyr)
library('pheatmap')
library(RColorBrewer)
#Reads data into table, adds row names and deletes the first column
dat<-read.table("Total_depth_avg_mag.txt", header = T)
row.names(dat) <- dat$mag
dat <- dat[, -1]
# Produces annotation data_frame from input file
data_annot_2 <- read.table("Mag_annot_taxonomy.txt", header = T)
rownames(data_annot_2) = data_annot_2$mag
data_annot <- data_annot_2["Taxonomy"]
#Produces annotated heatmap
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax.png", width =20,
height =30, border_color= NA, annotation_row = data_annot)
Which produces the following:
Heatmap_with_generic_colours
As there are quite a few (34) variables in my annotations some of them end up having the same colours so I would like to use my own palette. I used the following code to try to do this:
#Making a version of the "Greys" set from Rcolorbrewer containing 17 colours
coul = brewer.pal(9, "Greys")
coul = colorRampPalette(coul)(17)
#Producing a palette to feed into pheatmap. Contains 34 colours.
my_palette <- c(brewer.pal(9, "Reds")[c(6)], brewer.pal(9, "Greens")
[c(4,7)], brewer.pal(9, "Oranges")[c(4)], brewer.pal(9, "Blues")[c(3,5,7)],
brewer.pal(8, "Accent")[c(4)], brewer.pal(8, "Accent")[c(6)], brewer.pal(8,
"Accent")[c(7)], coul, brewer.pal(9, "Purples")[c(3,4,5,7)], brewer.pal(9,
"BuGn")[c(3,4)], brewer.pal(8, "Pastel2")[c(7)])
#Producing annotated heatmap with my_palette
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax_col.png", width =20,
height =30, border_color= NA, annotation_row = data_annot,
annotation_colors = my_palette)
I then get the error "Error in annotation_colors[[names(annotation)[i]]] <- factor_colors[ind] : more elements supplied than there are to replace"
I'm not sure why this is as my_palette definitely has 34 colours in it and my annotation should contain 34 variables.
Can anyone suggest anything to fix this?
r pheatmap
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
I am a relative R newbie and am having some issues trying to change the colour palette used for annotations in pheatmap.
I have created an annotated heatmap from the file Total_depth_avg_mag.txt using the following commands:
library(vegan)
library(gplots)
library(dplyr)
library('pheatmap')
library(RColorBrewer)
#Reads data into table, adds row names and deletes the first column
dat<-read.table("Total_depth_avg_mag.txt", header = T)
row.names(dat) <- dat$mag
dat <- dat[, -1]
# Produces annotation data_frame from input file
data_annot_2 <- read.table("Mag_annot_taxonomy.txt", header = T)
rownames(data_annot_2) = data_annot_2$mag
data_annot <- data_annot_2["Taxonomy"]
#Produces annotated heatmap
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax.png", width =20,
height =30, border_color= NA, annotation_row = data_annot)
Which produces the following:
Heatmap_with_generic_colours
As there are quite a few (34) variables in my annotations some of them end up having the same colours so I would like to use my own palette. I used the following code to try to do this:
#Making a version of the "Greys" set from Rcolorbrewer containing 17 colours
coul = brewer.pal(9, "Greys")
coul = colorRampPalette(coul)(17)
#Producing a palette to feed into pheatmap. Contains 34 colours.
my_palette <- c(brewer.pal(9, "Reds")[c(6)], brewer.pal(9, "Greens")
[c(4,7)], brewer.pal(9, "Oranges")[c(4)], brewer.pal(9, "Blues")[c(3,5,7)],
brewer.pal(8, "Accent")[c(4)], brewer.pal(8, "Accent")[c(6)], brewer.pal(8,
"Accent")[c(7)], coul, brewer.pal(9, "Purples")[c(3,4,5,7)], brewer.pal(9,
"BuGn")[c(3,4)], brewer.pal(8, "Pastel2")[c(7)])
#Producing annotated heatmap with my_palette
pheatmap(dat, cluster_cols = F, cluster_rows = F, fontsize_col = 10,
fontsize_row = 5, filename = "Mags_all_unclustered_tax_col.png", width =20,
height =30, border_color= NA, annotation_row = data_annot,
annotation_colors = my_palette)
I then get the error "Error in annotation_colors[[names(annotation)[i]]] <- factor_colors[ind] : more elements supplied than there are to replace"
I'm not sure why this is as my_palette definitely has 34 colours in it and my annotation should contain 34 variables.
Can anyone suggest anything to fix this?
r pheatmap
r pheatmap
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
asked Nov 23 '18 at 14:31
SomebodyatthedoorSomebodyatthedoor
11
11
add a comment |
add a comment |
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