Comments (3)
labelframe<-data %>%
select(starts_with("cov"),binID) %>%
filter(!is.na(binID)) %>%
group_by(binID) %>%
replace(., is.na(.), 0) %>%
summarise_all(funs(mean))
mmplot(...)+
geom_text_repel(
data = labelframe,
aes(label=binID),
nudge_x = 1,
segment.size = 0.2,
segment.color = "grey50",
direction = "y",
hjust = 1,
size=5
)
from mmgenome2.
Something like this, where you just specify a column with groups?
library(mmgenome2)
#> Loading required package: ggplot2
mmsubset <- mmextract(mmgenome2,
data.frame(cov_C13.11.25 = c(1.253, 1.298, 2.78, 3.006, 1.772),
cov_C14.01.09 = c(46.774, 26.499, 15.013, 28.049, 48.58))
)
#> 185 scaffolds (or 2.39% of the scaffolds in mm, weighted by length) remain after 97100 of 97285 scaffolds have been filtered.
bin1 <- mmextract(mmsubset,
data.frame(cov_C13.11.25 = c(1.239, 1.273, 1.732, 2.075, 1.658),
cov_C14.01.09 = c(30.96, 41.872, 45.587, 40.788, 31.734))
)
#> 54 scaffolds (or 53.19% of the scaffolds in mm, weighted by length) remain after 131 of 185 scaffolds have been filtered.
bin2 <- mmextract(mmsubset,
data.frame(cov_C13.11.25 = c(2.052, 2.479, 2.874, 2.527),
cov_C14.01.09 = c(20.203, 29.722, 25.62, 17.494))
)
#> 41 scaffolds (or 43.23% of the scaffolds in mm, weighted by length) remain after 144 of 185 scaffolds have been filtered.
mmsubset$bin <- NA
mmsubset$bin[which(mmsubset$scaffold %in% bin1$scaffold)] <- "bin1"
mmsubset$bin[which(mmsubset$scaffold %in% bin2$scaffold)] <- "bin2"
mmplot(mmsubset,
x = "cov_C13.11.25",
y = "cov_C14.01.09",
label_bins = "bin")
Created on 2018-10-03 by the reprex package (v0.2.1)
from mmgenome2.
Main addition is this
from mmgenome2.
Related Issues (20)
- mmplot to support color by correlation to a selected contig
- mmnetwork breaks when running on big datasets
- specify color range
- mmnetwork with highlight_labels and scaffold_labels = T show labels twice
- Can you put a link in the home page about where the data for the example comes from? HOT 8
- mmplot_cov_profiles highlight option HOT 1
- mmplot_cov_profiles pass scaffold names to plotly
- mmextract does not work with integers HOT 2
- mmplot - selection HOT 2
- extract.fastq.for.reassembly.pl: Use of uninitialized value HOT 1
- mmgenome2 installing with R 3.6.0 HOT 3
- add function to plot GC skew HOT 3
- mmplot coverage heatmap HOT 4
- mmplot coverage ordination
- install on mac os, R 3.6.1 HOT 2
- Failed to install it in R4.0 HOT 3
- mmexport to make linux line ends
- Running mmstats on big assemblies cause integer overflow
- shiny not supported on M1 HOT 1
- Umap instead of tsne as non-linear dimension reduction HOT 1
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from mmgenome2.