Error in gheatmap (ggtree package): “Error: Must request at least one colour from a hue palette.”
1
The last line gives an error:
library(ggtree)
nwk <- read.tree("nwk_file")
metadata <- read.table("metadata_file", sep="t", stringsAsFactor=FALSE)
g <- ggtree(nwk)
gheatmap(g, metadata, offset=5, width=0.5, font.size=3, colnames_angle=-45,
hjust=0)
The error reads:
"Error: Must request at least one colour from a hue palette."
I checked and the gheatmap function has default parameters for colours.
EDIT
I tried to make a reproducible example:
library(ggtree)
tree_nwk <- "(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,
((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
write(tree_nwk, file = "data.nwk")
tree <- read.tree("data.nwk")
p <- ggtree(tree)
dd <- data.frame(taxa = LETTERS[1:13],
place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))
dd <- dd[sample(1:13, 13), ]
row.names(dd) <- NULL
write(t(dd), "test_data.txt", ncolumns = 3, append = FALSE, sep = "t")
test_table <- read.table("test_data.txt", sep="t", stringsAsFactor=F)
gheatmap(p, test_table, offset=5, width=0.5, font.size=3,
colnames_angle=-45, hjust=0)
r bioconductor ggtree
asked Nov 21 '18 at 19:04
orenrivorenriv
62
add a comment |
1
The last line gives an error:
library(ggtree)
nwk <- read.tree("nwk_file")
metadata <- read.table("metadata_file", sep="t", stringsAsFactor=FALSE)
g <- ggtree(nwk)
gheatmap(g, metadata, offset=5, width=0.5, font.size=3, colnames_angle=-45,
hjust=0)
The error reads:
"Error: Must request at least one colour from a hue palette."
I checked and the gheatmap function has default parameters for colours.
EDIT
I tried to make a reproducible example:
library(ggtree)
tree_nwk <- "(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,
((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
write(tree_nwk, file = "data.nwk")
tree <- read.tree("data.nwk")
p <- ggtree(tree)
dd <- data.frame(taxa = LETTERS[1:13],
place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))
dd <- dd[sample(1:13, 13), ]
row.names(dd) <- NULL
write(t(dd), "test_data.txt", ncolumns = 3, append = FALSE, sep = "t")
test_table <- read.table("test_data.txt", sep="t", stringsAsFactor=F)
gheatmap(p, test_table, offset=5, width=0.5, font.size=3,
colnames_angle=-45, hjust=0)
r bioconductor ggtree
asked Nov 21 '18 at 19:04
orenrivorenriv
62
1
Could you add a reproducible example?
– paoloeusebi
Nov 21 '18 at 22:04
add a comment |
1
1
1
The last line gives an error:
library(ggtree)
nwk <- read.tree("nwk_file")
metadata <- read.table("metadata_file", sep="t", stringsAsFactor=FALSE)
g <- ggtree(nwk)
gheatmap(g, metadata, offset=5, width=0.5, font.size=3, colnames_angle=-45,
hjust=0)
The error reads:
"Error: Must request at least one colour from a hue palette."
I checked and the gheatmap function has default parameters for colours.
EDIT
I tried to make a reproducible example:
library(ggtree)
tree_nwk <- "(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,
((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
write(tree_nwk, file = "data.nwk")
tree <- read.tree("data.nwk")
p <- ggtree(tree)
dd <- data.frame(taxa = LETTERS[1:13],
place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))
dd <- dd[sample(1:13, 13), ]
row.names(dd) <- NULL
write(t(dd), "test_data.txt", ncolumns = 3, append = FALSE, sep = "t")
test_table <- read.table("test_data.txt", sep="t", stringsAsFactor=F)
gheatmap(p, test_table, offset=5, width=0.5, font.size=3,
colnames_angle=-45, hjust=0)
r bioconductor ggtree
asked Nov 21 '18 at 19:04
orenrivorenriv
62
The last line gives an error:
library(ggtree)
nwk <- read.tree("nwk_file")
metadata <- read.table("metadata_file", sep="t", stringsAsFactor=FALSE)
g <- ggtree(nwk)
gheatmap(g, metadata, offset=5, width=0.5, font.size=3, colnames_angle=-45,
hjust=0)
The error reads:
"Error: Must request at least one colour from a hue palette."
I checked and the gheatmap function has default parameters for colours.
EDIT
I tried to make a reproducible example:
library(ggtree)
tree_nwk <- "(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,
((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);"
write(tree_nwk, file = "data.nwk")
tree <- read.tree("data.nwk")
p <- ggtree(tree)
dd <- data.frame(taxa = LETTERS[1:13],
place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))
dd <- dd[sample(1:13, 13), ]
row.names(dd) <- NULL
write(t(dd), "test_data.txt", ncolumns = 3, append = FALSE, sep = "t")
test_table <- read.table("test_data.txt", sep="t", stringsAsFactor=F)
gheatmap(p, test_table, offset=5, width=0.5, font.size=3,
colnames_angle=-45, hjust=0)
r bioconductor ggtree
r bioconductor ggtree
asked Nov 21 '18 at 19:04
orenrivorenriv
62
asked Nov 21 '18 at 19:04
orenrivorenriv
62
edited Nov 22 '18 at 9:15
orenriv
asked Nov 21 '18 at 19:04
orenrivorenriv
62
asked Nov 21 '18 at 19:04
orenrivorenriv
62
asked Nov 21 '18 at 19:04
orenrivorenriv
62
62
1
Could you add a reproducible example?
– paoloeusebi
Nov 21 '18 at 22:04
add a comment |
1
Could you add a reproducible example?
– paoloeusebi
Nov 21 '18 at 22:04
1
1
Could you add a reproducible example?
– paoloeusebi
Nov 21 '18 at 22:04
Could you add a reproducible example?
– paoloeusebi
Nov 21 '18 at 22:04
add a comment |
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1
Could you add a reproducible example?
– paoloeusebi
Nov 21 '18 at 22:04