Problem with background probabilites as matrix
gcambray opened this issue · 0 comments
gcambray commented
Hi there,
thanks for this excellent package
I'm trying to provide a dataframe as input for the bg argument with the following call:
logomaker(selected, type = "EDLogo", bg = bg_freq)
but the std messages tells me:
using a background with equal probability for all symbols
Analyzing the positional frequency matrix
color_type not provided, so switching to per_row option for
color_type
using a background with equal probability for all symbols
frame width not provided, taken to be 1
frame width not provided, taken to be 1
So it looks like it is not recognizing the matrix as a correct input
Tried reducing the matrix to a vector with eg
logomaker(selected, type = "EDLogo", bg = apply(bg_freq, 1, median)
and this works fine
The bg_freq
matrix I'm using looks like this:
> bg_freq
X1 X2 X3 X4
A 0.05279903 0.04980073 0.05216351 0.05247792
R 0.07329378 0.07228652 0.07226239 0.07359076
N 0.03852414 0.04015821 0.03832839 0.03770225
D 0.03353948 0.03509813 0.03223993 0.03155547
C 0.03961352 0.04219518 0.04243954 0.04012201
E 0.02266077 0.02258770 0.02070860 0.02267954
Q 0.02168435 0.02120837 0.01836090 0.02008950
G 0.06898353 0.06675281 0.07242395 0.07669331
H 0.03605946 0.03450182 0.03327166 0.03264350
I 0.04746946 0.04550153 0.05004575 0.04720432
L 0.09994603 0.09670940 0.09729298 0.09461981
K 0.02239764 0.02331004 0.02001609 0.02170547
M 0.02649304 0.02574321 0.02573282 0.02503830
F 0.05888548 0.06087385 0.06871872 0.06445573
P 0.04518813 0.04547472 0.04307440 0.04472590
S 0.09771599 0.09989207 0.09634974 0.09773208
T 0.04927112 0.05092396 0.05147100 0.04962240
W 0.02641661 0.02564366 0.02608376 0.02669080
Y 0.04525383 0.04639751 0.04625036 0.04635929
V 0.07226708 0.07094374 0.07230865 0.07268440
STOP 0.02153753 0.02399685 0.02045687 0.02160725
The selected
input looks like this:
> selected
X1 X2 X3 X4
A 4391 312 18522 36137
R 1892 448 19556 754
N 15031 69 14746 9056
D 79066 8 20538 28701
C 6862 100 5082 5329
E 20854 1 11766 30431
Q 6055 3 15775 18050
G 2804 181 11035 3275
H 25443 2350 7719 14401
I 7118 6464 17796 4061
L 20541 49420 33519 30211
K 1706 57 12112 749
M 5246 8809 10347 8940
F 27814 94952 6160 6547
P 13 231 7385 8387
S 28827 252 36469 49113
T 13302 5898 24544 24978
W 8027 8266 2746 1192
Y 30918 138029 7065 12714
V 11667 1750 34702 24573
STOP 48 25 41 26
Is there something wrong with my input or is that a bug?
Thanks for your help!