I have a data matrix called mymat. Below is the code I have used to plot the graph for the samples (key.related.sheet). What I need now is to change the colour of the lines that fall within the IBS range of 0.8-1.5 into blue, 0.4-0.6 in red and 0.1- (-0.1) in yellow and anything below -0.1 in green. How can we do this?
code
library(data.table)
library(ggplot2)
library(dplyr)
cpp <- melt(as.data.table(mymat), measure = patterns("^IBS", "^Num_Good"),
value.name = c("IBS", "Num_Good")) %>%
.[, c("IBS", "Num_Good") := lapply(.SD, as.numeric), .SDcols = IBS:Num_Good]
ggplot(cpp, aes(x = Num_Good, y = IBS, col = key.related.sheet)) +
geom_line() +
#geom_vline(xintercept = 0)+
geom_hline(yintercept = 0)+
geom_hline(yintercept = 0.5)+
geom_hline(yintercept = 1.0)+
scale_colour_discrete(guide = FALSE)
data
mymat<- structure(c("AOGC-02-0010:AOGC-02-0010", "AOGC-02-0010:AOGC-02-0022",
"AOGC-02-0010:AOGC-02-0063", "AOGC-02-0010:AOGC-02-0079", "AOGC-02-0010:AOGC-02-0087",
"AOGC-02-0010:AOGC-02-0105", "AOGC-02-0010:AOGC-02-0108", "AOGC-02-0010:AOGC-02-0112",
"AOGC-02-0010:AOGC-02-0118", "AOGC-02-0010:AOGC-02-0161", "AOGC-02-0010:AOGC-02-0509",
"AOGC-02-0010:AOGC-02-0512", "AOGC-02-0010:AOGC-02-0513", "AOGC-02-0010:AOGC-02-0522",
"AOGC-02-0010:AOGC-02-0523", "AOGC-02-0010:AOGC-03-0094", "AOGC-02-0010:AOGC-03-0114",
"AOGC-02-0010:AOGC-03-0122", "AOGC-02-0010:AOGC-03-0132", "AOGC-02-0010:AOGC-03-0138",
"AOGC-02-0010:AOGC-05-0009", "1.12", "-0.00346", "0.0132", "0.0238",
"0.00404", "-0.0201", "-0.00653", "-0.00466", "-0.00942", "-0.00484",
"-0.0085", "-0.00231", "-0.03", "-0.0235", "-0.00412", "-0.0025",
"-0.0111", "0.000753", "-0.0231", "-0.0205", "-0.0121", "67289",
"52782", "51066", "46950", "47943", "51516", "59956", "57771",
"52397", "58087", "54291", "33791", "24889", "65773", "65777",
"51710", "55043", "50168", "64144", "64580", "57970", "1.13",
"0.500283", "0.0108", "0.0227", "0.400507", "-0.0219", "-0.00914",
"0.800371", "-0.0147", "-0.00372", "-0.00817", "-0.00983", "-0.0248",
"-0.0205", "-0.012", "-0.0127", "-0.0107", "0.0106", "-0.026",
"-0.023", "-0.900788", "53519", "42192", "40667", "37442", "38262",
"40952", "47671", "45966", "41675", "46191", "43512", "27316",
"20038", "52297", "52304", "41075", "43963", "39989", "51040",
"51390", "46087", "1.12", "-0.00143", "0.00778", "0.0119", "0.00842",
"-0.0237", "-0.0168", "0.00345", "-0.0112", "0.00414", "-0.00337",
"-0.0097", "-0.0322", "-0.0275", "-0.0173", "-0.017", "-0.0081",
"0.0256", "-0.0327", "-0.00254", "-0.0166", "26864", "21262",
"20553", "18909", "19335", "20543", "23915", "23002", "20917",
"23130", "22233", "14524", "10685", "26261", "26244", "20542",
"22356", "20132", "25647", "25777", "23045", "1.15", "0.00715",
"-0.00543", "0.0192", "0.0254", "-0.00775", "-0.00167", "0.00523",
"-0.027", "0.0125", "0.00182", "-0.0262", "-0.0526", "-0.0178",
"-0.0413", "-0.00793", "-0.00371", "0.0287", "-0.0141", "-0.00325",
"-0.0199", "13923", "10935", "10434", "9755", "9929", "10669",
"12505", "11958", "10818", "12048", "11064", "6635", "4757",
"13599", "13612", "10740", "11252", "10394", "13261", "13371",
"12042", "1.14", "-0.0122", "0.0103", "0.0189", "0.04", "0.0084",
"0.0227", "-0.0101", "-0.0328", "-0.0134", "-0.00669", "-0.0421",
"-0.0442", "-0.00531", "-0.044", "0.0526", "-0.00056", "0.0221",
"0.0182", "0.0259", "-0.0362", "7240", "5750", "5535", "5151",
"5202", "5567", "6525", "6231", "5618", "6291", "5892", "3645",
"2674", "7084", "7084", "5567", "5962", "5481", "6925", "7004",
"6279", "1.18", "0.0143", "-0.0763", "-0.00882", "0.0526", "-0.0195",
"-0.0531", "-0.00064", "-0.00616", "-0.00746", "0.0173", "-0.0795",
"0.0041", "0.018", "-0.0522", "0.0767", "0.0476", "0.000252",
"0.0456", "0.0377", "-0.0391", "3527", "2766", "2691", "2487",
"2461", "2672", "3135", "3010", "2680", "3056", "2846", "1707",
"1265", "3444", "3444", "2682", "2886", "2638", "3366", "3402",
"2982"), .Dim = c(21L, 13L), .Dimnames = list(c("1", "2", "3",
"4", "5", "6", "7", "8", "9", "10", "30", "31", "32", "33", "34",
"35", "36", "37", "38", "39", "40"), c("key.related.sheet", "IBS_from:1305328SNPS",
"Num_Good_SNPs_A:1305328SNPS", "IBS_from:1030725SNPS", "Num_Good_SNPs_A:1030725SNPS",
"IBS_from:514953SNPS", "Num_Good_SNPs_A:514953SNPS", "IBS_from:257361SNPS",
"Num_Good_SNPs_A:257361SNPS", "IBS_from:128603SNPS", "Num_Good_SNPs_A:128603SNPS",
"IBS_from:64000SNPS", "Num_Good_SNPs_A:64000SNPS")))
if you want to change the color of only sections of the line then you can add in something like this:
cpp$cutoff = cut(cpp$IBS,
breaks = c(-Inf, -0.1, 0.1, 0.4, 0.6, 0.8, 1.5),
labels = c("GREEN", "YELLOW", "GREY", "RED", "BLACK", "BLUE"))
and then plot like this:
ggplot(cpp, aes(x = Num_Good, y = IBS, group = key.related.sheet, color = cutoff)) +
geom_line() + geom_point()+
#geom_vline(xintercept = 0)+
geom_hline(yintercept = 0)+
geom_hline(yintercept = 0.5)+
geom_hline(yintercept = 1.0)+
scale_colour_discrete(guide = FALSE)
To make the entire lines the same color it depends on what color you which to adopt and the rules around that.
But you would probably group and summarise the data for that.
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