plotting_funcs.R does not visualize a plot with Warning messages:

[farhan-lab]

Hello,

I am trying to visualize the output files generated by treemix using plotting_funcs.R, But have'nt been able to make any plot. I am a beginner biologist in R, therefore could not really understand what I am doing wrong. I even tried with the example2.treemix.gz data, but get the same warning messages as follows:
Warning messages:
1: In plot_tree("TreeMix") : NAs introduced by coercion
2: In plot_tree("TreeMix") : NAs introduced by coercion
3: In plot_tree("TreeMix") : NAs introduced by coercion
4: In plot_tree("TreeMix") : NAs introduced by coercion

I run the analysis in the following steps following your protocol:
treemix -i example2.treemix.gz -k 500 -root YRI -m 1

source("plotting_funcs.R")
plot_tree("TreeMix")

V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 1 CHB NOT_ROOT NOT_MIG TIP 2 NA NA NA NA
2 2 NOT_ROOT NOT_MIG NOT_TIP 32 1 1 16 2
3 3 YRI NOT_ROOT NOT_MIG TIP 33 NA NA NA NA
4 4 CEU NOT_ROOT NOT_MIG TIP 16 NA NA NA NA
5 15 GIH NOT_ROOT NOT_MIG TIP 16 NA NA NA NA
6 16 NOT_ROOT NOT_MIG NOT_TIP 2 15 1 4 1
7 31 MKK NOT_ROOT NOT_MIG TIP 32 NA NA NA NA
8 32 NOT_ROOT NOT_MIG NOT_TIP 33 31 1 2 3
9 33 ROOT NOT_MIG NOT_TIP 33 3 1 32 4
10 34 NOT_ROOT MIG NOT_TIP 16 4 NA NA NA
V11 x y ymin ymax
1 CHB:0.0193834 0.059500866 0.5 0.4 0.6
2 (CHB:0.0193834,(GIH:0.00123639,CEU:0.00876907):0.0037504):0.0394214 0.040117466 0.4 0.0 0.6
3 YRI:0.000696066 0.000696066 0.9 0.8 1.0
4 CEU:0.00876907 0.052636936 0.1 0.0 0.2
5 GIH:0.00123639 0.045104256 0.3 0.2 0.4
6 (GIH:0.00123639,CEU:0.00876907):0.0037504 0.043867866 0.2 0.0 0.4
7 MKK:0.00565817 0.004058773 0.7 0.6 0.8
8 (MKK:0.00565817,(CHB:0.0193834,(GIH:0.00123639,CEU:0.00876907):0.0037504):0.0394214):0.000696066 0.000696066 0.6 0.0 0.8
9 (YRI:0.000696066,(MKK:0.00565817,(CHB:0.0193834,(GIH:0.00123639,CEU:0.00876907):0.0037504):0.0394214):0.000696066); 0.000000000 0.8 0.0 1.0
10 0.052636936 NA 0.0 0.2
[1] "1 0.043867866 0.052636936"
[1] 0.059500866 0.000696066 0.052636936 0.045104256 0.004058773
[1] 0.003
[1] "mse 0.000276775"
$d
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 1 CHB NOT_ROOT NOT_MIG TIP 2 NA NA NA NA
2 2 NOT_ROOT NOT_MIG NOT_TIP 32 1 1 16 2
3 3 YRI NOT_ROOT NOT_MIG TIP 33 NA NA NA NA
4 4 CEU NOT_ROOT NOT_MIG TIP 16 NA NA NA NA
5 15 GIH NOT_ROOT NOT_MIG TIP 16 NA NA NA NA
6 16 NOT_ROOT NOT_MIG NOT_TIP 2 15 1 4 1
7 31 MKK NOT_ROOT NOT_MIG TIP 32 NA NA NA NA
8 32 NOT_ROOT NOT_MIG NOT_TIP 33 31 1 2 3
9 33 ROOT NOT_MIG NOT_TIP 33 3 1 32 4
10 34 NOT_ROOT MIG NOT_TIP 16 4 NA NA NA
V11 x y ymin ymax
1 CHB:0.0193834 0.059500866 0.5 0.4 0.6
2 (CHB:0.0193834,(GIH:0.00123639,CEU:0.00876907):0.0037504):0.0394214 0.040117466 0.4 0.0 0.6
3 YRI:0.000696066 0.000696066 0.9 0.8 1.0
4 CEU:0.00876907 0.052636936 0.1 0.0 0.2
5 GIH:0.00123639 0.045104256 0.3 0.2 0.4
6 (GIH:0.00123639,CEU:0.00876907):0.0037504 0.043867866 0.2 0.0 0.4
7 MKK:0.00565817 0.004058773 0.7 0.6 0.8
8 (MKK:0.00565817,(CHB:0.0193834,(GIH:0.00123639,CEU:0.00876907):0.0037504):0.0394214):0.000696066 0.000696066 0.6 0.0 0.8
9 (YRI:0.000696066,(MKK:0.00565817,(CHB:0.0193834,(GIH:0.00123639,CEU:0.00876907):0.0037504):0.0394214):0.000696066); 0.000000000 0.8 0.0 1.0
10 0.052636936 0.1 0.0 0.2

$e
V1 V2 V3 V4 V5 V6 V7
1 2 1 0.019383400 1.000000 NOT_MIG 0 1.00000
2 32 31 0.003362707 0.770915 NOT_MIG 0 0.59431
3 32 2 0.039421400 1.000000 NOT_MIG 0 1.00000
4 2 16 0.003750400 1.000000 NOT_MIG 0 1.00000
5 33 3 0.000696066 1.000000 NOT_MIG 0 1.00000
6 33 32 0.000696066 1.000000 NOT_MIG 0 1.00000
7 16 15 0.001236390 1.000000 NOT_MIG 0 1.00000
8 16 34 0.008769070 1.000000 NOT_MIG 0 1.00000
9 34 4 0.000000000 1.000000 NOT_MIG 1 1.00000
10 34 31 0.000000000 0.229085 MIG 1 0.00000

Warning messages:
1: In plot_tree("TreeMix") : NAs introduced by coercion
2: In plot_tree("TreeMix") : NAs introduced by coercion
3: In plot_tree("TreeMix") : NAs introduced by coercion
4: In plot_tree("TreeMix") : NAs introduced by coercion

I would appreciate your help in this issue.
Thanks in advance!
Farhan