Entering edit mode
2.7 years ago
mohammedtoufiq91
▴
260
Hi,
I am working with an log2 fold change expression matrix in R and trying to plot a heatmap annotated with bars on each column on the top from the counts data (or responsive genes) using library(ComplexHeatmap) package and getting an error. I have provided the input data and expected out below. Please advise on how to solve this.
Error: number of observations in top annotation should be as same as ncol of the matrix.
Thank you, Toufiq
dput(Expression)
structure(c(-0.883643926, -0.248614376, -0.518091486, -0.535221236,
-0.415450436, -0.940323826, -0.723796576, -0.824290276, -0.753322836,
-0.806255146, -0.747521326, NA, -0.320247786, 0.110402434, -1.005757776,
-0.706686256, -0.796173776, -0.574616976, -0.757579476, -0.651924848,
-0.044501908, -0.451601548, -0.384956008, -0.678620408, -0.706674058,
-0.572657338, -0.686018538, -0.514713298, -0.532390248, -0.462136378,
NA, -0.123749828, 0.343669412, -0.489804678, -0.447612948, -0.611873538,
-0.477327798, -0.590774288, -0.017798089, 0.192058061, -0.055408169,
-0.152159119, 0.263042701, -0.382693409, -0.063857699, -0.152939869,
-0.050295909, -0.337659179, -0.058902499, NA, -0.410700949, -0.079817359,
-0.313859499, 0.002403881, -0.562811849, -0.353911149, 0.006032581,
-0.141324408, 0.096038562, 0.171087962, -0.295921938, 0.482199712,
-0.317140358, -0.115931318, -0.264788018, -0.158997338, -0.476858598,
0.039648912, NA, -0.235496858, 0.065630452, -0.175745228, 0.083321692,
-0.712253838, -0.251200888, -0.004567068, -0.167945369, 0.805406021,
-0.591077759, 0.741171721, 2.494610191, -0.532343489, -0.358607189,
-0.442774239, -0.103589789, 0.213156301, -0.022826199, NA, 1.215920941,
3.377354481, 0.033402621, -0.183228609, 0.616853471, 1.260055211,
-0.518548419, -0.269887464, 0.651177556, -0.638584884, 0.637445626,
2.363311126, -0.518550644, -0.548715454, -0.656370694, -0.150589014,
0.061194616, -0.121604684, NA, 1.198130706, 3.132598336, -0.102222284,
-0.338918174, 0.407338406, 1.192401486, -0.629295034, 0.224167264,
0.181754044, 0.271578844, -0.357815996, 0.173898274, 0.097649164,
0.047596544, 0.204227434, 0.047299374, 0.225855454, 0.098997764,
NA, 0.316586394, 0.050782324, 0.253073784, 0.266165624, 0.079117194,
0.031888764, 0.231072844, 0.055545271, 0.059685561, 0.006279711,
-0.635848059, 0.297302061, -0.006876539, -0.050632179, 0.006454301,
-0.042377289, -0.020155689, -0.125523179, NA, 0.207185861, 0.298005181,
0.050015221, 0.096842111, -0.226106489, -0.312930109, 0.042911411
), .Dim = c(19L, 8L), .Dimnames = list(c("Gene_1", "Gene_2",
"Gene_3", "Gene_4", "Gene_5", "Gene_6", "Gene_7", "Gene_8", "Gene_9",
"Gene_10", "Gene_11", "Gene_12", "Gene_13", "Gene_14", "Gene_15",
"Gene_16", "Gene_17", "Gene_18", "Gene_19"), c("A", "B", "C",
"D", "E", "F", "F1", "H")))
#> A B C D E
#> Gene_1 -0.8836439 -0.65192485 -0.017798089 -0.141324408 -0.16794537
#> Gene_2 -0.2486144 -0.04450191 0.192058061 0.096038562 0.80540602
#> Gene_3 -0.5180915 -0.45160155 -0.055408169 0.171087962 -0.59107776
#> Gene_4 -0.5352212 -0.38495601 -0.152159119 -0.295921938 0.74117172
#> Gene_5 -0.4154504 -0.67862041 0.263042701 0.482199712 2.49461019
#> Gene_6 -0.9403238 -0.70667406 -0.382693409 -0.317140358 -0.53234349
#> Gene_7 -0.7237966 -0.57265734 -0.063857699 -0.115931318 -0.35860719
#> Gene_8 -0.8242903 -0.68601854 -0.152939869 -0.264788018 -0.44277424
#> Gene_9 -0.7533228 -0.51471330 -0.050295909 -0.158997338 -0.10358979
#> Gene_10 -0.8062551 -0.53239025 -0.337659179 -0.476858598 0.21315630
#> Gene_11 -0.7475213 -0.46213638 -0.058902499 0.039648912 -0.02282620
#> Gene_12 NA NA NA NA NA
#> Gene_13 -0.3202478 -0.12374983 -0.410700949 -0.235496858 1.21592094
#> Gene_14 0.1104024 0.34366941 -0.079817359 0.065630452 3.37735448
#> Gene_15 -1.0057578 -0.48980468 -0.313859499 -0.175745228 0.03340262
#> Gene_16 -0.7066863 -0.44761295 0.002403881 0.083321692 -0.18322861
#> Gene_17 -0.7961738 -0.61187354 -0.562811849 -0.712253838 0.61685347
#> Gene_18 -0.5746170 -0.47732780 -0.353911149 -0.251200888 1.26005521
#> Gene_19 -0.7575795 -0.59077429 0.006032581 -0.004567068 -0.51854842
#> F F1 H
#> Gene_1 -0.26988746 0.22416726 0.055545271
#> Gene_2 0.65117756 0.18175404 0.059685561
#> Gene_3 -0.63858488 0.27157884 0.006279711
#> Gene_4 0.63744563 -0.35781600 -0.635848059
#> Gene_5 2.36331113 0.17389827 0.297302061
#> Gene_6 -0.51855064 0.09764916 -0.006876539
#> Gene_7 -0.54871545 0.04759654 -0.050632179
#> Gene_8 -0.65637069 0.20422743 0.006454301
#> Gene_9 -0.15058901 0.04729937 -0.042377289
#> Gene_10 0.06119462 0.22585545 -0.020155689
#> Gene_11 -0.12160468 0.09899776 -0.125523179
#> Gene_12 NA NA NA
#> Gene_13 1.19813071 0.31658639 0.207185861
#> Gene_14 3.13259834 0.05078232 0.298005181
#> Gene_15 -0.10222228 0.25307378 0.050015221
#> Gene_16 -0.33891817 0.26616562 0.096842111
#> Gene_17 0.40733841 0.07911719 -0.226106489
#> Gene_18 1.19240149 0.03188876 -0.312930109
#> Gene_19 -0.62929503 0.23107284 0.042911411
dput(Counts)
structure(list(A = 3L, B = 3L, C = 15L, D = 12L, E = 5L, F = 1L,
F1 = 7L, H = 5L), class = "data.frame", row.names = "counts")
#> A B C D E F F1 H
#> counts 3 3 15 12 5 1 7 5
all(colnames(Expression) == colnames(Counts))
# Plot heatmap
column_ha = HeatmapAnnotation(bar = anno_barplot(Counts))
Heatmap(Expression, name = "log2FC", top_annotation = column_ha, cluster_columns = F)
> Error: number of observations in top annotation should be as same as
> ncol of the matrix.
Expected plot
Created on 2022-04-21 by the [reprex package](https://reprex.tidyverse.org) (v2.0.1)
The problem comes from the fact Counts is not numeric but a data.frame.
But next problem, you'll have to deal with is the presence of NA in your dataframe...
Hi Basti, thank you for the prompt response. This resolved my query.