I was wondering whether it is possible to add a geom_smooth (or any trend-line) to a geom_col barplot in ggplot2. Here is the code I’m using:
library(dplyr)
library(readxl)
library(ggplot2)
library(RColorBrewer)
mapQ_prop <- read_excel("/path/to.file.xlsm", 16)
mapQ_prop <- mapQ_prop %>% arrange(value)
mapQ_prop$sample <- as.vector(mapQ_prop$sample)
mapQ_prop$sample = factor(mapQ_prop$sample,mapQ_prop$sample)
plot_mapQ <-
ggplot(data=mapQ_prop, aes(x=sample, y=value, fill=brewer.pal(9, "Blues")[5])) + geom_col(color="black", alpha=.75) + theme_bw() +
theme(legend.title=element_text(face='italic'), legend.position='bottom', legend.direction='horizontal') +
scale_fill_manual(values=brewer.pal(9, "Blues")[5], labels="value") +
guides(
fill=guide_legend(title="proportion over Q20", title.position="top", title.hjust=.5)
) +
xlab("")
plot_mapQ + theme(axis.text.x=element_text(angle=90, vjust=0.5, hjust=1, size=6)) +
scale_y_continuous(expand=c(0,0), limits=c(0,1))
and a dput of the data to recreate the dataset:
structure(list(sample = structure(1:279, levels = c("HGDP00749",
"HGDP01172", "HGDP00936", "HGDP00533", "TZ-11", "AV-21", "HGDP01286",
"HGDP01036", "HGDP00982", "mixe0007", "HGDP01076", "IHW9118",
"HGDP00546", "HGDP01308", "IHW9193", "HGDP00775", "HGDP01015",
"HGDP01153", "HGDP00783", "HGDP00125", "Peru60", "HGDP01344",
"HGDP00124", "Jordan445", "TGBS21", "Bu16", "NA17385", "HGDP00887",
"HGDP01320", "I3", "Y4", "HG02494", "NA00726", "HGDP01163", "HGDP01228",
"HGDP00543", "HGDP00555", "IraqiJew4291", "YemeniteJew5433",
"NA17386", "HGDP01198", "HGDP01032", "HGDP01179", "CHI-034",
"HGDP01098", "HGDP01335", "HGDP00541", "HGDP00956", "HGDP01250",
"M13", "HGDP01044", "HGDP01306", "HGDP01191", "tdj409_shugnan",
"ND15865", "KD4", "SAH41", "CHI-007", "DNK07", "HGDP00550", "K4",
"NA15728", "Bu5", "HGDP01333", "HGDP00987", "NA13607", "HGDP00737",
"M4", "B11", "Sir19", "NA13604", "NA15763", "Nesk_22", "NorthOssetia5",
"HGDP01188", "IraqiJew1771", "Bishkek28440", "HGDP01350", "HGDP00058",
"Y8", "HGDP00545", "ML2", "NA15761", "HGDP00090", "K1", "I1",
"HG00360", "NA11200", "HGDP01355", "Igor21", "R6", "HGDP01168",
"Dus22", "HGDP00660", "Dus16", "ML3", "Esk29", "HGDP01079", "HGDP00476",
"ND19394", "HGDP01297", "HGDP00706", "Sir40", "YemeniteJew4695",
"R3", "HGDP00852", "NA13616", "HGDP00725", "HG00174", "HGDP01223",
"HGDP00449", "HGDP01401", "HGDP01246", "Nlk3", "SAH31", "altai363p",
"HGDP00526", "B17", "HGDP00547", "HGDP01211", "HGDP00195", "SA0722",
"NA17374", "HGDP01240", "Ale14", "tdj430_shugnan", "HG00190",
"NA21490", "Nlk1", "HGDP00569", "HG01503", "HGDP00216", "HGDP01095",
"HGDP00702", "HGDP00857", "mixa0105", "Ale32", "HGDP00846", "HGDP00785",
"HGDP01315", "HGDP00540", "HG03007", "HGDP00552", "HG00126",
"NA17377", "Tuba19", "HGDP01314", "NA11201", "HG02724", "Nesk_25",
"zapo0098", "HGDP01203", "Bishkek28439", "NA18940", "Est400",
"HGDP00554", "mg31", "HGDP00798", "HGDP00722", "HGDP01018", "HG00128",
"HG02783", "Ul5", "Kor82", "HGDP00548", "HGDP00855", "HGDP01078",
"NOR111", "Mansi41", "DNK11", "Mansi79", "HGDP00019", "HGDP00796",
"Utsa21", "mixe0002", "Armenian222", "HGDP01345", "HGDP01417",
"Kayseri24424", "Kusunda02", "HGDP00656", "Kayseri23827", "Igor20",
"mg27", "HG02574", "mixe0042", "HG02790", "HG03006", "HGDP00286",
"NA19044", "NA21581", "SA0342", "NorthOssetia12", "HGDP01242",
"HG03100", "HGDP00530", "HGDP00428", "HGDP01312", "HGDP00027",
"Est375", "HGDP00208", "HGDP00549", "HGDP00328", "abh107", "zapo0099",
"HGDP00553", "HGDP00951", "HG01846", "HGDP01402", "HGDP01253",
"Ale20", "Ayodo_81S", "BulgarianB4", "Nlk18", "HG02464", "HGDP00932",
"HGDP00773", "Kusunda15", "BulgarianC1", "armenia293", "HGDP00616",
"HG01504", "DNK05", "HGDP01365", "mixa0099", "HG01600", "HGDP01274",
"HGDP00551", "NA19023", "iran11", "ALB212", "Ale22", "HGDP00160",
"HGDP01364", "HGDP01012", "HG02943", "HGDP01323", "abh100", "Tuba9",
"Sam02", "HGDP01215", "Ul31", "HG03078", "Ayodo_430C", "HGDP00597",
"lez49", "HGDP00474", "Ayodo_502C", "lez42", "ch113", "HGDP00157",
"HGDP01338", "HGDP00650", "HGDP00556", "HGDP01199", "NA15203",
"HGDP01047", "HGDP00903", "Sir26", "Jordan603", "NA15202", "iran17",
"HGDP00232", "Utsa22", "HG03085", "HGDP01035", "Jordan214", "HGDP01034",
"HGDP00991", "HGDP00713", "HGDP00928", "HGDP00338", "HGDP00457",
"HGDP00717", "HGDP01414", "HGDP00461", "HGDP01030", "HGDP01028",
"HGDP00915"), class = "factor"), value = c(0.568026, 0.586163,
0.611686, 0.615131, 0.617185, 0.622274, 0.626596, 0.634903, 0.638516,
0.642894, 0.645012, 0.646246, 0.646643, 0.651504, 0.659362, 0.66035,
0.693463, 0.748575, 0.775585, 0.799904, 0.809495, 0.810797, 0.813196,
0.815898, 0.828594, 0.830746, 0.831749, 0.839394, 0.851589, 0.854254,
0.855906, 0.856021, 0.85647, 0.857044, 0.857156, 0.857976, 0.858112,
0.858384, 0.858926, 0.860694, 0.860702, 0.860986, 0.861457, 0.861628,
0.862806, 0.863012, 0.863729, 0.864315, 0.864371, 0.864374, 0.865234,
0.865495, 0.86583, 0.866675, 0.866983, 0.868242, 0.869689, 0.869762,
0.869845, 0.870519, 0.870821, 0.871134, 0.871593, 0.871753, 0.871931,
0.873242, 0.87332, 0.873374, 0.87366, 0.87414, 0.874163, 0.874369,
0.87446, 0.874509, 0.874528, 0.874643, 0.874838, 0.87535, 0.875595,
0.875707, 0.876403, 0.876409, 0.876425, 0.876552, 0.876586, 0.876844,
0.87685, 0.876926, 0.876986, 0.877308, 0.877446, 0.877482, 0.877994,
0.878208, 0.878836, 0.878899, 0.87894, 0.879029, 0.879148, 0.879171,
0.879554, 0.879579, 0.879708, 0.879831, 0.880295, 0.880383, 0.880435,
0.880438, 0.880496, 0.880511, 0.880531, 0.880572, 0.880714, 0.880739,
0.880881, 0.881043, 0.881261, 0.881282, 0.881284, 0.881339, 0.881367,
0.881484, 0.881486, 0.88157, 0.881974, 0.881982, 0.882005, 0.882182,
0.882322, 0.882348, 0.882413, 0.882549, 0.882566, 0.88257, 0.882615,
0.88282, 0.88289, 0.88296, 0.882994, 0.883129, 0.883145, 0.883264,
0.883329, 0.883363, 0.883431, 0.883586, 0.883737, 0.88375, 0.883824,
0.884139, 0.884221, 0.884251, 0.88438, 0.88438, 0.884433, 0.884435,
0.884652, 0.884653, 0.884655, 0.884817, 0.884844, 0.885007, 0.885098,
0.885134, 0.885139, 0.885225, 0.885253, 0.885263, 0.885312, 0.885339,
0.885368, 0.885419, 0.885469, 0.885578, 0.885686, 0.885717, 0.885723,
0.885762, 0.885836, 0.885843, 0.885872, 0.88603, 0.886063, 0.886112,
0.886188, 0.886225, 0.886261, 0.886298, 0.886304, 0.88641, 0.886415,
0.886488, 0.88649, 0.886531, 0.886567, 0.886641, 0.886672, 0.886673,
0.886703, 0.886772, 0.886801, 0.886898, 0.886928, 0.886931, 0.887006,
0.887128, 0.887154, 0.887189, 0.887366, 0.887373, 0.887508, 0.887675,
0.887703, 0.887736, 0.887782, 0.887811, 0.88784, 0.887906, 0.888032,
0.888162, 0.888187, 0.888203, 0.888264, 0.888264, 0.888365, 0.888382,
0.888386, 0.888428, 0.888446, 0.888484, 0.888519, 0.888545, 0.888584,
0.888627, 0.888649, 0.888734, 0.888886, 0.888915, 0.888999, 0.889029,
0.889035, 0.889068, 0.889124, 0.889333, 0.889496, 0.889727, 0.889898,
0.890081, 0.890192, 0.890197, 0.89028, 0.890416, 0.890417, 0.890432,
0.890526, 0.890692, 0.890903, 0.890929, 0.890992, 0.891027, 0.891045,
0.891088, 0.891198, 0.891241, 0.891266, 0.891418, 0.891555, 0.891697,
0.891863, 0.891935, 0.892073, 0.892172, 0.892176, 0.892227, 0.892872,
0.892909, 0.892915, 0.893008, 0.893234)), row.names = c(NA, -279L
), class = c("tbl_df", "tbl", "data.frame"))
Now, one thing might be at the root of this issue is not having numerical data on the x-axis; if so, it is still feasible somehow?
Also, I added the three lines before the actual plot as looking up a bit it appears to be one solution to sort the categorical values on the x-axis in ascending order based on their value on the y-axis. If anyone has any idea, any help is much appreciated, thanks!
>Solution :
To plot categories in a specific order, it’s typical to use factors like you have here. If we use as.numeric(some_factor), we’ll get the ordering, which we could use for geom_smooth. The span parameter of stats::loess controls the degree of smoothing, which I’ve set manually here to follow this data more closely.
...
geom_smooth(aes(x = as.numeric(sample)), method = "loess", span = 0.1) +
...
