CODEWITHSUNDEEP
rggplot2data-visualizationggpubr
Michael Bale
Michael Bale

Reputation: 11

Error Adding p-value to parallel coordinates plot (ggplot)

I have a data set that is paired data from multiple samples that I want to do a parallel coordinates graph with and include a p-value above (i.e. plot each data point in each group and link the pairs with a line and have the comparison statistic above the plotted data).

I can get the graph to (largely) look the way I want it to, but when I try and add a p-value using stat_compare_means(paired=TRUE), I get 3 errors:

2 x:

"Don't know how to automatically pick scale for object of type quosure/formula. Defaulting to continuous."

1 x:

"Error in validDetails.text(x) : 'pairlist' object cannot be coerced to type 'double'".

My data is a data.frame with three variables: a sample variable so I know which pair is which, a group variable so I know which category the value is, and the value variable. I've pasted the code below and am more than happy to take other suggestions on any other ways to make the code look better as well.

ggplot(test_OCI, aes(x=test_OCI$variable, y=test_OCI$value, group =test_OCI$Pt)) +
  geom_point(aes(x=test_OCI$variable),size=3)+
  geom_line(aes(x=test_OCI$variable),group=test_OCI$Pt)+
  theme_bw()+
  theme(panel.border=element_blank(), 
        panel.grid.major=element_blank(),
        panel.grid.minor=element_blank(), 
        axis.line=element_line(color="black"))+
  scale_x_discrete(labels=c("OCI_pre_ART"="Pre-ART OCI", "OCI_on_ART"="On-ART OCI"))+
  stat_compare_means(paired=TRUE)

edit 1: adding sample data

There isn't too much data, but I've added it below per request.

    Pt  variable    value
1   Pt1 OCI_pre_ART 0.024
2   Pt2 OCI_pre_ART 0.027
3   Pt3 OCI_pre_ART 0.027
4   Pt4 OCI_pre_ART 0.010
5   Pt5 OCI_pre_ART 0.075
6   Pt6 OCI_pre_ART 0.040
7   Pt7 OCI_pre_ART 0.070
8   Pt8 OCI_pre_ART 0.011
9   Pt9 OCI_pre_ART 0.022
10 Pt10 OCI_pre_ART 0.006
11 Pt11 OCI_pre_ART 0.019
12  Pt1  OCI_on_ART 0.223
13  Pt2  OCI_on_ART 0.166
14  Pt3  OCI_on_ART 0.163
15  Pt4  OCI_on_ART 0.126
16  Pt5  OCI_on_ART 0.090
17  Pt6  OCI_on_ART 0.139
18  Pt7  OCI_on_ART 0.403
19  Pt8  OCI_on_ART 0.342
20  Pt9  OCI_on_ART 0.092

edit 2: packages

all lines in the figure code are from ggplot2 except stat_compare_means(paired=TRUE) which is from ggpubr.

Upvotes: 0

Views: 150

Answers (1)

Michael Bale
Michael Bale

Reputation: 11

I'm not sure if this is the reason, but it appears that the stat_compare_means() line was not interpreting the x~y aesthestic. Changing the line to stat_compare_means(comparisons = list(c("OCI_pre_ART","OCI_on_ART")), paired=TRUE) resulted in a functional graph.

Upvotes: 1

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