Change legend title and legend labels in "plot_ordination"

[mr2raccoon]

Hey,

I drew a Bray-curtis ordination plot but I cannot change any specifications in the legend.

 phy.ord <- ordinate(physeq_comp, "NMDS", "bray")
p1<-  plot_ordination(physeq_comp, phy.ord, type="samples", color="sampleID")+
    geom_point(size=5)+
    scale_color_manual(values=pale)+
     ggtitle("Bray-Curtis-Index")

All usual ggplot arguments fail: likep1 <- p1 + guides(fill=guide_legend(title="New Legend Title")) or labs("title")

Did anyone experience the same problem and knows a way around?

[ycl6]

@mr2raccoon Instead of fill, you need to use color, so you can use one of the following to change legend title:

# example dataset
data(GlobalPatterns)
ord <- ordinate(GlobalPatterns, "NMDS", "bray")

# using guides
plot_ordination(GlobalPatterns, ord, type = "samples", color = "SampleType") +
        guides(color = guide_legend(title = "New Legend Title")) +
        geom_point(size=5) + ggtitle("Bray-Curtis-Index")

# using labs
plot_ordination(GlobalPatterns, ord, type = "samples", color = "SampleType") +
        geom_point(size = 5) + labs(title = "Bray-Curtis-Index", color = "New Legend Title")

[mr2raccoon]

Thanks I could change the title- But how to change the annotation for each point inside the legend? I tried p1 + guides(color=guide_legend(title="Probe", values = c("Illumina MB5", "Nanopore MB5", "Illumina MB6","Nanopore MB6" )))

and p1 + guides(color=guide_legend(title="Probe", labels = c("Illumina MB5", "Nanopore MB5", "Illumina MB6","Nanopore MB6" )))

[ycl6]

@mr2raccoon I would suggest you rename the labels in the Sample Data, it saves you the trouble to change it again and again in all the rest of the plots. Using the example data:

# Check your Sample Data structure
> sample_data(GlobalPatterns)[1:10]
Sample Data:        [10 samples by 7 sample variables]:
        X.SampleID  Primer Final_Barcode Barcode_truncated_plus_T Barcode_full_length SampleType                                Description
CL3            CL3 ILBC_01        AACGCA                   TGCGTT         CTAGCGTGCGT       Soil   Calhoun South Carolina Pine soil, pH 4.9
CC1            CC1 ILBC_02        AACTCG                   CGAGTT         CATCGACGAGT       Soil   Cedar Creek Minnesota, grassland, pH 6.1
SV1            SV1 ILBC_03        AACTGT                   ACAGTT         GTACGCACAGT       Soil Sevilleta new Mexico, desert scrub, pH 8.3
M31Fcsw    M31Fcsw ILBC_04        AAGAGA                   TCTCTT         TCGACATCTCT      Feces    M3, Day 1, fecal swab, whole body study
M11Fcsw    M11Fcsw ILBC_05        AAGCTG                   CAGCTT         CGACTGCAGCT      Feces   M1, Day 1, fecal swab, whole body study 
M31Plmr    M31Plmr ILBC_07        AATCGT                   ACGATT         CGAGTCACGAT       Skin    M3, Day 1, right palm, whole body study
M11Plmr    M11Plmr ILBC_08        ACACAC                   GTGTGT         GCCATAGTGTG       Skin   M1, Day 1, right palm, whole body study 
F21Plmr    F21Plmr ILBC_09        ACACAT                   ATGTGT         GTAGACATGTG       Skin  F1, Day 1,  right palm, whole body study 
M31Tong    M31Tong ILBC_10        ACACGA                   TCGTGT         TGTGGCTCGTG     Tongue       M3, Day 1, tongue, whole body study 
M11Tong    M11Tong ILBC_11        ACACGG                   CCGTGT         TAGACACCGTG     Tongue       M1, Day 1, tongue, whole body study 

# Check if SampleType is a factor variable
> is.factor(sample_data(GlobalPatterns)$SampleType)
[1] TRUE

# Given SampleType is a factor variable, check the levels
> levels(sample_data(GlobalPatterns)$SampleType)
[1] "Feces"              "Freshwater"         "Freshwater (creek)" "Mock"               "Ocean"              "Sediment (estuary)" "Skin"              
[8] "Soil"               "Tongue"            

# Change labels
levels(sample_data(GlobalPatterns)$SampleType) = c("Human 1", "Env 1", "Env 2", "Mock", "Env 3", "Env 4", "Human 2", "Env 5", "Human 3")

# SampleType labels is now updated
> sample_data(GlobalPatterns)[1:10]
Sample Data:        [10 samples by 7 sample variables]:
        X.SampleID  Primer Final_Barcode Barcode_truncated_plus_T Barcode_full_length SampleType                                Description
CL3            CL3 ILBC_01        AACGCA                   TGCGTT         CTAGCGTGCGT      Env 5   Calhoun South Carolina Pine soil, pH 4.9
CC1            CC1 ILBC_02        AACTCG                   CGAGTT         CATCGACGAGT      Env 5   Cedar Creek Minnesota, grassland, pH 6.1
SV1            SV1 ILBC_03        AACTGT                   ACAGTT         GTACGCACAGT      Env 5 Sevilleta new Mexico, desert scrub, pH 8.3
M31Fcsw    M31Fcsw ILBC_04        AAGAGA                   TCTCTT         TCGACATCTCT    Human 1    M3, Day 1, fecal swab, whole body study
M11Fcsw    M11Fcsw ILBC_05        AAGCTG                   CAGCTT         CGACTGCAGCT    Human 1   M1, Day 1, fecal swab, whole body study 
M31Plmr    M31Plmr ILBC_07        AATCGT                   ACGATT         CGAGTCACGAT    Human 2    M3, Day 1, right palm, whole body study
M11Plmr    M11Plmr ILBC_08        ACACAC                   GTGTGT         GCCATAGTGTG    Human 2   M1, Day 1, right palm, whole body study 
F21Plmr    F21Plmr ILBC_09        ACACAT                   ATGTGT         GTAGACATGTG    Human 2  F1, Day 1,  right palm, whole body study 
M31Tong    M31Tong ILBC_10        ACACGA                   TCGTGT         TGTGGCTCGTG    Human 3       M3, Day 1, tongue, whole body study 
M11Tong    M11Tong ILBC_11        ACACGG                   CCGTGT         TAGACACCGTG    Human 3       M1, Day 1, tongue, whole body study 

If you want to keep the original labels, you can create a new column to store the new labels you wish to use, and use that in all your plots. Using the example data:

# Create a new column NewSampleType with the same labels as SampleType
sample_data(GlobalPatterns)$NewSampleType = sample_data(GlobalPatterns)$SampleType

# Change the labels
levels(sample_data(GlobalPatterns)$NewSampleType) = c("Human 1", "Env 1", "Env 2", "Mock", "Env 3", "Env 4", "Human 2", "Env 5", "Human 3")

# Plot
plot_ordination(GlobalPatterns, ord, type = "samples", color = "NewSampleType") +
        guides(color = guide_legend(title = "New Legend Title")) +
        geom_point(size = 5) + ggtitle("Bray-Curtis-Index")