How do I change the size of the points based on the value of the column using ggplot?
0
Using ggplot on rstudio, I am trying to change the size of the point of my scatter plot based on the log of the pvalue column. This is how my matrix looks like.
head(BDpvalue)
id t-value pvalue mean.f mean.m Gene Chromosome
1 ILMN_1212619 3.0512842692996 0.00938046962249251 85.40076 80.02744 Mfap3l 8
2 ILMN_1212693 3.40887110529531 0.00452088152864021 87.28189 82.89533 Snx33 9
3 ILMN_1213324 -4.54750670298688 0.000414140589714275 82.68924 88.81421 Zfp961 8
4 ILMN_1213848 -3.63180275429357 0.00246745595956587 421.61780 469.51845 Itgb1bp1 12
5 ILMN_1213961 2.97573716869553 0.00960659647288939 82.01748 78.44721 Copg2 6
6 ILMN_1214482 -4.23666060706341 0.000813240203181102 136.55021 153.34681 2700081O15Rik 19
>
The code to change the size based on the log of the pvalue column seems correct to me, but for some reason I am not seeing a change in the graph, this is the code that I used.
ggplot(BDpvalue, aes(x=(log(mean.m,10)+log(mean.f,10))/2,
y= log(mean.f/mean.m,10),color=Chromosome) + geom_point(aes(size=(-log(pvalue,10))))
r ggplot2
edited Nov 12 '18 at 1:17
NelsonGon
846217
asked Nov 12 '18 at 1:13
151
11
|
show 1 more comment
0
Using ggplot on rstudio, I am trying to change the size of the point of my scatter plot based on the log of the pvalue column. This is how my matrix looks like.
head(BDpvalue)
id t-value pvalue mean.f mean.m Gene Chromosome
1 ILMN_1212619 3.0512842692996 0.00938046962249251 85.40076 80.02744 Mfap3l 8
2 ILMN_1212693 3.40887110529531 0.00452088152864021 87.28189 82.89533 Snx33 9
3 ILMN_1213324 -4.54750670298688 0.000414140589714275 82.68924 88.81421 Zfp961 8
4 ILMN_1213848 -3.63180275429357 0.00246745595956587 421.61780 469.51845 Itgb1bp1 12
5 ILMN_1213961 2.97573716869553 0.00960659647288939 82.01748 78.44721 Copg2 6
6 ILMN_1214482 -4.23666060706341 0.000813240203181102 136.55021 153.34681 2700081O15Rik 19
>
The code to change the size based on the log of the pvalue column seems correct to me, but for some reason I am not seeing a change in the graph, this is the code that I used.
ggplot(BDpvalue, aes(x=(log(mean.m,10)+log(mean.f,10))/2,
y= log(mean.f/mean.m,10),color=Chromosome) + geom_point(aes(size=(-log(pvalue,10))))
r ggplot2
edited Nov 12 '18 at 1:17
NelsonGon
846217
asked Nov 12 '18 at 1:13
151
11
please post a reproducible dataset withdput()
– the_darkside
Nov 12 '18 at 1:24
3
Your parentheses are wrong;geom_pointshould be outside ofggplot:ggplot(BDpvalue, aes(x = (log(mean.m, 10) + log(mean.f, 10))/2, y = log(mean.f/mean.m,10), color = Chromosome)) + geom_point(aes(size = -log(pvalue,10)))
– alistaire
Nov 12 '18 at 1:28
I tried using the code from above and got an error message: Error in Math.factor(pvalue, 10) : ‘log’ not meaningful for factors
– 151
Nov 12 '18 at 1:53
1
tryBDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)
– passiflora
Nov 12 '18 at 3:35
@passiflora,BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)will return the factor levels. To get the original numerical values of the factor useBDpvalue$pvalue <-as.numeric(as.character(BDpvalue$pvalue))
– Niek
Nov 12 '18 at 7:47
|
show 1 more comment
0
0
0
Using ggplot on rstudio, I am trying to change the size of the point of my scatter plot based on the log of the pvalue column. This is how my matrix looks like.
head(BDpvalue)
id t-value pvalue mean.f mean.m Gene Chromosome
1 ILMN_1212619 3.0512842692996 0.00938046962249251 85.40076 80.02744 Mfap3l 8
2 ILMN_1212693 3.40887110529531 0.00452088152864021 87.28189 82.89533 Snx33 9
3 ILMN_1213324 -4.54750670298688 0.000414140589714275 82.68924 88.81421 Zfp961 8
4 ILMN_1213848 -3.63180275429357 0.00246745595956587 421.61780 469.51845 Itgb1bp1 12
5 ILMN_1213961 2.97573716869553 0.00960659647288939 82.01748 78.44721 Copg2 6
6 ILMN_1214482 -4.23666060706341 0.000813240203181102 136.55021 153.34681 2700081O15Rik 19
>
The code to change the size based on the log of the pvalue column seems correct to me, but for some reason I am not seeing a change in the graph, this is the code that I used.
ggplot(BDpvalue, aes(x=(log(mean.m,10)+log(mean.f,10))/2,
y= log(mean.f/mean.m,10),color=Chromosome) + geom_point(aes(size=(-log(pvalue,10))))
r ggplot2
edited Nov 12 '18 at 1:17
NelsonGon
846217
asked Nov 12 '18 at 1:13
151
11
Using ggplot on rstudio, I am trying to change the size of the point of my scatter plot based on the log of the pvalue column. This is how my matrix looks like.
head(BDpvalue)
id t-value pvalue mean.f mean.m Gene Chromosome
1 ILMN_1212619 3.0512842692996 0.00938046962249251 85.40076 80.02744 Mfap3l 8
2 ILMN_1212693 3.40887110529531 0.00452088152864021 87.28189 82.89533 Snx33 9
3 ILMN_1213324 -4.54750670298688 0.000414140589714275 82.68924 88.81421 Zfp961 8
4 ILMN_1213848 -3.63180275429357 0.00246745595956587 421.61780 469.51845 Itgb1bp1 12
5 ILMN_1213961 2.97573716869553 0.00960659647288939 82.01748 78.44721 Copg2 6
6 ILMN_1214482 -4.23666060706341 0.000813240203181102 136.55021 153.34681 2700081O15Rik 19
>
The code to change the size based on the log of the pvalue column seems correct to me, but for some reason I am not seeing a change in the graph, this is the code that I used.
ggplot(BDpvalue, aes(x=(log(mean.m,10)+log(mean.f,10))/2,
y= log(mean.f/mean.m,10),color=Chromosome) + geom_point(aes(size=(-log(pvalue,10))))
r ggplot2
r ggplot2
edited Nov 12 '18 at 1:17
NelsonGon
846217
asked Nov 12 '18 at 1:13
151
11
edited Nov 12 '18 at 1:17
NelsonGon
846217
asked Nov 12 '18 at 1:13
151
11
edited Nov 12 '18 at 1:17
NelsonGon
846217
edited Nov 12 '18 at 1:17
NelsonGon
846217
edited Nov 12 '18 at 1:17
NelsonGon
846217
846217
asked Nov 12 '18 at 1:13
151
11
asked Nov 12 '18 at 1:13
151
11
asked Nov 12 '18 at 1:13
151
11
11
please post a reproducible dataset withdput()
– the_darkside
Nov 12 '18 at 1:24
3
Your parentheses are wrong;geom_pointshould be outside ofggplot:ggplot(BDpvalue, aes(x = (log(mean.m, 10) + log(mean.f, 10))/2, y = log(mean.f/mean.m,10), color = Chromosome)) + geom_point(aes(size = -log(pvalue,10)))
– alistaire
Nov 12 '18 at 1:28
I tried using the code from above and got an error message: Error in Math.factor(pvalue, 10) : ‘log’ not meaningful for factors
– 151
Nov 12 '18 at 1:53
1
tryBDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)
– passiflora
Nov 12 '18 at 3:35
@passiflora,BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)will return the factor levels. To get the original numerical values of the factor useBDpvalue$pvalue <-as.numeric(as.character(BDpvalue$pvalue))
– Niek
Nov 12 '18 at 7:47
|
show 1 more comment
please post a reproducible dataset withdput()
– the_darkside
Nov 12 '18 at 1:24
3
Your parentheses are wrong;geom_pointshould be outside ofggplot:ggplot(BDpvalue, aes(x = (log(mean.m, 10) + log(mean.f, 10))/2, y = log(mean.f/mean.m,10), color = Chromosome)) + geom_point(aes(size = -log(pvalue,10)))
– alistaire
Nov 12 '18 at 1:28
I tried using the code from above and got an error message: Error in Math.factor(pvalue, 10) : ‘log’ not meaningful for factors
– 151
Nov 12 '18 at 1:53
1
tryBDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)
– passiflora
Nov 12 '18 at 3:35
@passiflora,BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)will return the factor levels. To get the original numerical values of the factor useBDpvalue$pvalue <-as.numeric(as.character(BDpvalue$pvalue))
– Niek
Nov 12 '18 at 7:47
please post a reproducible dataset with
dput()– the_darkside
Nov 12 '18 at 1:24
please post a reproducible dataset with
dput()– the_darkside
Nov 12 '18 at 1:24
3
3
Your parentheses are wrong;
geom_point should be outside of ggplot: ggplot(BDpvalue, aes(x = (log(mean.m, 10) + log(mean.f, 10))/2, y = log(mean.f/mean.m,10), color = Chromosome)) + geom_point(aes(size = -log(pvalue,10)))– alistaire
Nov 12 '18 at 1:28
Your parentheses are wrong;
geom_point should be outside of ggplot: ggplot(BDpvalue, aes(x = (log(mean.m, 10) + log(mean.f, 10))/2, y = log(mean.f/mean.m,10), color = Chromosome)) + geom_point(aes(size = -log(pvalue,10)))– alistaire
Nov 12 '18 at 1:28
I tried using the code from above and got an error message: Error in Math.factor(pvalue, 10) : ‘log’ not meaningful for factors
– 151
Nov 12 '18 at 1:53
I tried using the code from above and got an error message: Error in Math.factor(pvalue, 10) : ‘log’ not meaningful for factors
– 151
Nov 12 '18 at 1:53
1
1
try
BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)– passiflora
Nov 12 '18 at 3:35
try
BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)– passiflora
Nov 12 '18 at 3:35
@passiflora,
BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue) will return the factor levels. To get the original numerical values of the factor use BDpvalue$pvalue <-as.numeric(as.character(BDpvalue$pvalue))– Niek
Nov 12 '18 at 7:47
@passiflora,
BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue) will return the factor levels. To get the original numerical values of the factor use BDpvalue$pvalue <-as.numeric(as.character(BDpvalue$pvalue))– Niek
Nov 12 '18 at 7:47
|
show 1 more comment
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please post a reproducible dataset with
dput()– the_darkside
Nov 12 '18 at 1:24
3
Your parentheses are wrong;
geom_pointshould be outside ofggplot:ggplot(BDpvalue, aes(x = (log(mean.m, 10) + log(mean.f, 10))/2, y = log(mean.f/mean.m,10), color = Chromosome)) + geom_point(aes(size = -log(pvalue,10)))– alistaire
Nov 12 '18 at 1:28
I tried using the code from above and got an error message: Error in Math.factor(pvalue, 10) : ‘log’ not meaningful for factors
– 151
Nov 12 '18 at 1:53
1
try
BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)– passiflora
Nov 12 '18 at 3:35
@passiflora,
BDpvalue$pvalue <- as.numeric(BDpvalue$pvalue)will return the factor levels. To get the original numerical values of the factor useBDpvalue$pvalue <-as.numeric(as.character(BDpvalue$pvalue))– Niek
Nov 12 '18 at 7:47