Increase space between x-axis factors in ggplot - r

I am using the geom_pointrange function in ggplot2 in order to plot the spread of some measurement over different condition for 5 subjects. In order not to have the subjects overlap I have constructed the plot as follows:
Final = structure(list(Subject = structure(c(1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L), .Label = c("1", "2", "3", "4", "5"), class = "factor"),
X00.conditionName = structure(c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 1L, 1L, 2L, 2L, 3L, 3L,
4L, 4L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 1L, 1L, 2L, 2L, 3L,
3L, 4L, 4L), .Label = c("EyeClose-Haptic", "mixed-Haptic_Visual",
"only-Haptic", "only-Visual"), class = "factor"), X03.totalTargetNumber = c(2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L,
2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L,
3L, 2L, 3L, 2L, 3L, 2L, 3L, 2L, 3L), Accuracy = c(0.075870763,
0.0907863686, 0.0222156611, 0.0492028585333333, 0.0301178471,
0.0736098328666667, 0.0329723832, 0.0455095300666667, 0.065151615,
0.0979033533333333, 0.0247176775, 0.0335825226666667, 0.027385248,
0.0462643053333333, 0.037272505, 0.0652166726666667, 0.043005086,
0.061848328, 0.031106749, 0.0275656054, 0.026701889, 0.0373967466666667,
0.028998468, 0.03219287, 0.0597213356, 0.0851717708333333,
0.030286913, 0.0779058462666667, 0.043368508, 0.051437624,
0.029002474, 0.0479204566666667, 0.094555739, 0.0856268291666667,
0.031908514, 0.0310441326666667, 0.036311762, 0.0496942306666667,
0.054625148, 0.0482682121666667), upperCI = c(0.116082073022708,
0.139632763787946, 0.0315087794760623, 0.0727058964327625,
0.0468512606854127, 0.116787586356955, 0.0444933233012107,
0.062820743812494, 0.0858551911272202, 0.136013260005381,
0.0327074347874691, 0.0460471773903695, 0.035302995136302,
0.0740077338495226, 0.0641795522210299, 0.131047110446756,
0.0572545979325947, 0.0809511078363974, 0.0414215170576924,
0.0341480438532189, 0.0382253716300962, 0.0519626825555577,
0.0377955915789704, 0.0430125127419472, 0.0903928001427357,
0.114245467448517, 0.0461054194398361, 0.129350863514659,
0.0635159480110737, 0.0717647837071829, 0.0371919026867606,
0.0615899295823839, 0.170222051412597, 0.128502458351433,
0.046712862081242, 0.0388340720489338, 0.0574188259607336,
0.0786845830951613, 0.0844193698576058, 0.0784830058409822
), lowerCI = c(0.0356594529772922, 0.0419399734120541, 0.0129225427239377,
0.0256998206339042, 0.0133844335145873, 0.0304320793763786,
0.0214514430987893, 0.0281983163208393, 0.0444480388727798,
0.059793446661286, 0.0167279202125309, 0.0211178679429639,
0.019467500863698, 0.0185208768171441, 0.0103654577789701,
-0.000613765113422152, 0.0287555740674053, 0.0427455481636026,
0.0207919809423076, 0.0209831669467811, 0.0151784063699038,
0.0228308107777757, 0.0202013444210296, 0.0213732272580528,
0.0290498710572643, 0.0560980742181497, 0.0144684065601638,
0.0264608290186746, 0.0232210679889263, 0.0311104642928171,
0.0208130453132394, 0.0342509837509495, 0.018889426587403,
0.0427511999819006, 0.017104165918758, 0.0232541932843995,
0.0152046980392664, 0.0207038782381721, 0.0248309261423941,
0.0180534184923511), CondLevel = c("EyeClose-Haptic2", "EyeClose-Haptic3",
"mixed-Haptic_Visual2", "mixed-Haptic_Visual3", "only-Haptic2",
"only-Haptic3", "only-Visual2", "only-Visual3", "EyeClose-Haptic2",
"EyeClose-Haptic3", "mixed-Haptic_Visual2", "mixed-Haptic_Visual3",
"only-Haptic2", "only-Haptic3", "only-Visual2", "only-Visual3",
"EyeClose-Haptic2", "EyeClose-Haptic3", "mixed-Haptic_Visual2",
"mixed-Haptic_Visual3", "only-Haptic2", "only-Haptic3", "only-Visual2",
"only-Visual3", "EyeClose-Haptic2", "EyeClose-Haptic3", "mixed-Haptic_Visual2",
"mixed-Haptic_Visual3", "only-Haptic2", "only-Haptic3", "only-Visual2",
"only-Visual3", "EyeClose-Haptic2", "EyeClose-Haptic3", "mixed-Haptic_Visual2",
"mixed-Haptic_Visual3", "only-Haptic2", "only-Haptic3", "only-Visual2",
"only-Visual3")), .Names = c("Subject", "X00.conditionName",
"X03.totalTargetNumber", "Accuracy", "upperCI", "lowerCI", "CondLevel"
), row.names = c(NA, -40L), class = "data.frame")
require(ggplot2)
pdf("Pilot2.pdf", w = 12, h = 8)
limits <- aes(ymax = upperCI, ymin=lowerCI)
BaseLayer = ggplot(data = Final, aes (x = X00.conditionName, y = Accuracy, color = Subject, group = Subject ))
BaseLayer + geom_pointrange(limits, position=position_dodge(width=1), size = 1.5) +
theme(axis.text=element_text(size=14), axis.title=element_text(size=14), axis.text.x = element_text(angle = 25, hjust = 1)) +
facet_grid (.~X03.totalTargetNumber) + ggtitle ("Pilot 2") + xlab ("Condition")
dev.off()
As you can see the x-axis is discrete, and the points are very "crowded", so that it is difficult to tell apart the different categories.
Is there a way to increase the space between the different categories ?

The best solutoin is to use facets to create 8 separate tall and skinny plots with all these features that are separated by a thin white gutter between them with a solid label at the top. You could keep or lose X-axis labels. It creates one figure of 8 graphs that communicates better than on big graph.
Like this:Stack-ggplot2-geom-pointrange-facet-grid-with-coord-flip
except yours would be verticle

Related

Plot linear regression analysis with error bar for variability

I wanted to make plots that look like figure 1 (source: link)
In figure 1, they have plotted the regression analysis with one-year yield variability. In my case, I would like to plot variability between two locations and 4 blocks for each treatment group. So the plot I wanted would have three facets for factors B.glucosidase, Protein, POX.C of variable and four colors for treatments factors. Also, in my current plot I have legend for block and treatment. I should only have treatment because the block should be used for making error bar for variability.
I tried with this code, which obviously doesn't work for what I want. (Data for df.melted included below.)
ggplot(df.melted, aes(x = value, y = yield, color = as.factor(treatment))) +
geom_point(aes(shape= as.factor(block))) +
stat_smooth(method = "lm", formula = y ~ x, col = "darkslategrey", se=F) +
stat_poly_eq(formula = y~x,
# aes(label = paste(..eq.label.., ..rr.label.., sep = "~~~")),
aes(label = ..rr.label..),
parse = TRUE) +
theme_classic() +
geom_errorbar(aes(ymax = df.melted$yield+sd(df.melted$yield), ymin = df.melted$yield-sd(df.melted$yield)), width = 0.05)+
facet_wrap(~variable)
Data:
df.melted <- structure(list(Location = structure(c(1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("M", "U"), class = "factor"),
treatment = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L,
3L, 3L, 3L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L), .Label = c("CC",
"CCS", "CS", "SCS"), class = "factor"), block = c(1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L,
1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L,
1L, 2L, 3L, 4L), yield = c(5156L, 5157L, 5551L, 5156L, 4804L,
4720L, 4757L, 5021L, 4826L, 4807L, 4475L, 4596L, 4669L, 4588L,
4542L, 4592L, 5583L, 5442L, 5693L, 5739L, 5045L, 4902L, 5006L,
5086L, 4639L, 4781L, 4934L, 4857L, 4537L, 4890L, 4842L, 4608L,
5156L, 5157L, 5551L, 5156L, 4804L, 4720L, 4757L, 5021L, 4826L,
4807L, 4475L, 4596L, 4669L, 4588L, 4542L, 4592L, 5583L, 5442L,
5693L, 5739L, 5045L, 4902L, 5006L, 5086L, 4639L, 4781L, 4934L,
4857L, 4537L, 4890L, 4842L, 4608L, 5156L, 5157L, 5551L, 5156L,
4804L, 4720L, 4757L, 5021L, 4826L, 4807L, 4475L, 4596L, 4669L,
4588L, 4542L, 4592L, 5583L, 5442L, 5693L, 5739L, 5045L, 4902L,
5006L, 5086L, 4639L, 4781L, 4934L, 4857L, 4537L, 4890L, 4842L,
4608L), variable = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("B.glucosidase",
"Protein", "POX.C"), class = "factor"), value = c(1.600946,
1.474084, 1.433078, 1.532492, 1.198667, 1.193193, 1.214941,
1.360981, 1.853056, 1.690117, 1.544357, 1.825132, 1.695409,
1.764123, 1.903743, 1.538684, 0.845077, 1.011463, 0.857032,
0.989803, 0.859022, 0.919467, 1.01717, 0.861689, 0.972332,
0.952922, 0.804431, 0.742634, 1.195837, 1.267285, 1.08571,
1.20097, 6212.631579, 5641.403509, 4392.280702, 7120.701754,
5305.964912, 4936.842105, 5383.157895, 6077.894737, 5769.122807,
5016.842105, 5060.350877, 5967.017544, 5576.842105, 5174.035088,
5655.438596, 5468.77193, 7933.333333, 7000, 6352.982456,
8153.684211, 6077.894737, 4939.649123, 5002.807018, 6489.122807,
4694.035088, 5901.052632, 4303.859649, 6768.421053, 6159.298246,
6090.526316, 4939.649123, 5262.45614, 810.3024, 835.5242,
856.206, 759.8589, 726.2298, 792.6472, 724.7165, 699.3266,
500.9153, 634.8698, 637.9536, 648.8814, 641.0357, 623.3822,
555.2834, 520.8119, 683.3528, 595.9173, 635.4315, 672.4234,
847.2944, 745.5665, 778.3548, 735.8141, 395.2647, 570.4148,
458.0383, 535.3851, 678.0293, 670.7419, 335.2923, 562.5674
)), row.names = c(NA, -96L), class = "data.frame")
library(dplyr)
library(ggplot2)
library(ggpmisc)
Summarize data frame (this could also be done with stat_summary(), but it's often clearer/more transparent to do it explicitly up front). (I think that because your data set is balanced you could collapse/average over the block structure first, and then do your whole plot with the reduced data set - it shouldn't change the outcome of the linear regressions at all, at least not the mean values ... and any statistical comparisons should probably done on block-level summaries anyway ...)
df.sum <- (df.melted
%>% group_by(Location,treatment,variable)
%>% summarise(value=mean(value),yield_sd=sd(yield),
## collapse yield to mean *after* computing sd!
yield=mean(yield))
)
Plot:
(ggplot(df.melted,
aes(x = value, y = yield, color = treatment))
+ stat_smooth(method = "lm", col = "darkslategrey", se=FALSE)
+ stat_poly_eq(
formula = y ~ x,
## aes(label = paste(..eq.label.., ..rr.label.., sep = "~~~")),
aes(group=1, label = ..rr.label..),
parse = TRUE)
+ theme_classic()
+ scale_shape(guide=FALSE)
+ geom_point(data=df.sum)
+ geom_errorbar(data=df.sum,
aes(ymax = yield+yield_sd, ymin = yield-yield_sd),
width = 0.05)
+ facet_wrap(~variable,scale="free_x")
)
(adding group=1 to the stat_poly_eq() aesthetics means we only plot a single R^2 value per facet)
Since you're no longer using the shape aesthetic for anything, you could consider using it to show the Location variable ...

Normalization of data within ggplot

I have my data as
melted.df <- structure(list(organisms = structure(c(1L, 1L, 1L, 2L, 3L, 3L,
3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L,
1L, 1L, 1L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 1L, 1L, 1L, 2L, 3L,
3L, 3L, 3L, 4L, 4L, 4L), .Label = c("Botrytis cinerea", "Fusarium graminearum",
"Human", "Mus musculus"), class = "factor"), types = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("AllMismatches",
"mismatchType2", "MismatchesType1", "totalDNA"), class = "factor"),
mutations = c(30501L, 12256L, 58357L, 366531L, 3475L, 186907L,
253453L, 222L, 24906L, 2775L, 247990L, 12324L, 4395L, 25324L,
77862L, 1862L, 112217L, 163117L, 100L, 17549L, 1057L, 20331L,
18177L, 7861L, 33033L, 288669L, 1613L, 74690L, 90336L, 122L,
7357L, 1718L, 227659L, 635951L, 229493L, 868052L, 2418724L,
65833L, 1081903L, 1339758L, 4318L, 59387L, 15199L, 2134229L
)), row.names = c(NA, -44L), class = "data.frame")
The values totalDNA in type column indicates total DNAs in the data whereas mismatches are the mutations. I would like to normalize this data based on totalDNA values and plot it. The way I am plotting right now doesn't give me the accurate picture of the data as todalDNA inflates the whole Y-axis and other three types(mismatchType2, mismatchesType1 and AllMismatches) are not properly visible with respect to totalDNA. What would be the better way to plot this? Should I first calculate the percentage? or Perhaps do log scaling? Thanks for helping me out.
ggplot(melted.df, aes(x = types, y = mutations, color=types)) +
geom_point()+
facet_grid(.~organisms)+
xlab("Types")+
ylab("Mismatches")+
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank())
Try a log scale?
ggplot(melted.df, aes(x = types, y = mutations, color=types)) +
geom_point()+
facet_grid(.~organisms)+
xlab("Types")+
ylab("Mismatches")+
# ylim(c(90,130))+
scale_y_log10()+ #add log scale
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank())
How would you normalise on total DNA? Would you use the (geometric) mean?

Order geom_lines from the highest to the lowest in each facet

I have a factor comp_id that has 4 levels (comp1 to comp4). I want to order each level from the highest to the lowest in a geom_line plot.
I got this plot
using this script
library(data.table)
library(ggplot2)
dat <- as.data.table(df)
dat[, ord := sprintf("%02i", frank(dat, comp_id, -value, ties.method = "first"))]
ggplot(dat, aes(x = ord, y = value , group = comp_id , colour = comp_id))+
geom_line()+
facet_wrap(~comp_id, ncol = 1, scales = "free_x", labeller = label_parsed, drop = TRUE)+
theme(axis.text.x=element_text(angle=35, vjust=1, hjust=1,
))
to replace x axis labels
+scale_x_discrete(labels = dat[, setNames(as.character(predictor), ord)])
As you can see, it worked fine for all levels except comp3 where variables ordered (100 to 105) were plotted at the start of facet where they were supposed to be plotted at the end. I wonder what went wrong. Any suggestions will be appreciated.
DATA
> dput(df)
structure(list(predictor = c("c_C2", "c_C3", "c_C4", "d_D2",
"d_D3", "d_D4", "d_D5", "h_BF", "h_BFI", "h_ER", "h_f", "h_PET",
"h_QuFl", "h_Ra", "l_Da", "l_NaCo", "l_ShBe", "m_a", "m_DrDe",
"m_ElRa", "m_MeElm", "m_MeSlPe", "Mr_Co", "Mr_GRAv", "Mr_GREy",
"Mr_Mu", "Mr_Sa", "s_SaLo", "s_SiLo", "s_sSiLo", "s_Stl", "Sr_Li",
"Sr_SaCoCoTe", "Sr_SaLoSi", "Sr_SaMubcl", "c_C2", "c_C3", "c_C4",
"d_D2", "d_D3", "d_D4", "d_D5", "h_BF", "h_BFI", "h_ER", "h_f",
"h_PET", "h_QuFl", "h_Ra", "l_Da", "l_NaCo", "l_ShBe", "m_a",
"m_DrDe", "m_ElRa", "m_MeElm", "m_MeSlPe", "Mr_Co", "Mr_GRAv",
"Mr_GREy", "Mr_Mu", "Mr_Sa", "s_SaLo", "s_SiLo", "s_sSiLo", "s_Stl",
"Sr_Li", "Sr_SaCoCoTe", "Sr_SaLoSi", "Sr_SaMubcl", "c_C2", "c_C3",
"c_C4", "d_D2", "d_D3", "d_D4", "d_D5", "h_BF", "h_BFI", "h_ER",
"h_f", "h_PET", "h_QuFl", "h_Ra", "l_Da", "l_NaCo", "l_ShBe",
"m_a", "m_DrDe", "m_ElRa", "m_MeElm", "m_MeSlPe", "Mr_Co", "Mr_GRAv",
"Mr_GREy", "Mr_Mu", "Mr_Sa", "s_SaLo", "s_SiLo", "s_sSiLo", "s_Stl",
"Sr_Li", "Sr_SaCoCoTe", "Sr_SaLoSi", "Sr_SaMubcl", "c_C2", "c_C3",
"c_C4", "d_D2", "d_D3", "d_D4", "d_D5", "h_BF", "h_BFI", "h_ER",
"h_f", "h_PET", "h_QuFl", "h_Ra", "l_Da", "l_NaCo", "l_ShBe",
"m_a", "m_DrDe", "m_ElRa", "m_MeElm", "m_MeSlPe", "Mr_Co", "Mr_GRAv",
"Mr_GREy", "Mr_Mu", "Mr_Sa", "s_SaLo", "s_SiLo", "s_sSiLo", "s_Stl",
"Sr_Li", "Sr_SaCoCoTe", "Sr_SaLoSi", "Sr_SaMubcl"), comp_id = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("comp1",
"comp2", "comp3", "comp4"), class = "factor"), value = c(0.0633325075111356,
-0.0193713154441617, 0.000785081075580719, 0.287610195287972,
-0.0913783988809322, -0.122928438782758, 0.305621459875726, 0.0356570047659489,
0.367574915852176, -0.240835821698893, 0.0035597425358522, 0.295952594554233,
-0.0439920206129066, -0.235580426938533, 0.191947159509267, -0.132931615006652,
0.065155805120025, 0.038311284807646, 0.187182963731454, 0.120969596703282,
-0.118935354491654, -0.173851183397175, 0.125870264508295, 0.158977975187947,
-0.209351605852615, -0.0231602829054583, 0.078383405846316, 0.0959455355349004,
0.238306328058919, -0.188667962455942, -0.138302814516594, -0.0586994514783439,
0.019524606432138, 0.210636138928319, -0.204454169255484, -0.149879080476447,
0.282741114373524, -0.272911905666994, 0.102508662574812, -0.35056583225677,
0.257262737814283, 0.202117594283655, 0.191773977367133, 0.298513575892895,
0.139576016330362, 0.165641757285727, -0.071542760140058, 0.116819894570386,
0.145104320521166, 0.126636637925691, 0.0810830011112734, -0.0949935353116725,
0.0785254958291791, 0.0326439188223452, 0.065833153228218, 0.155405435626813,
0.128737420120173, 0.214943178842044, -0.0210359058420932, 0.0117832135586799,
0.0762824228178598, -0.29145271973574, -0.17089908579109, -0.0992003952524557,
0.163749177828358, 0.196561728687348, 0.0951493527111932, 0.17238711709624,
0.0638301486629609, -0.0351097560634362, 0.0647994534663104,
-0.154895398844537, 0.186448424833243, 0.240881706707846, -0.241364320964797,
-0.089459273670017, 0.0491598702691844, -0.200660845431752, -0.0339722426751736,
0.131396251991635, -0.195471026941394, -0.05919918680627, -0.184160478394361,
0.129464190293723, 0.193021703469902, 0.178985522376368, -0.245966624042807,
-0.23478025602535, 0.198620462933836, -0.157573246492692, -0.00808698000885529,
0.0413693509741982, -0.121020524702316, 0.105148862728949, 0.214386790903084,
-0.204515275979768, -0.0906160054540168, -0.276985960928353,
0.0768294557774406, -0.074181085595352, 0.138680723918144, -0.119684214245213,
-0.0919678069134681, 0.322602153170851, 0.228878715511945, -0.433082572929477,
0.05754301130056, 0.130719232236558, 0.253999327778221, 0.0469683234741709,
-0.0258294537417061, -0.258318910865727, -0.00406472629347961,
-0.165003562015847, -0.0292142578447021, 0.00862320222199929,
0.0875367120866572, 0.0331716236283754, -0.0418387105725687,
-0.12523142839593, -0.200857915084298, 0.138378222132672, 0.00992811008724002,
-0.0201043482518474, -0.148894977354092, -0.323240591170999,
-0.0556713655820164, 0.379033571103569, -0.264420286734383, 0.127560649906739,
-0.00546455207923468, -0.203293330594455, -0.122085266718802,
-0.0970860819632599, -0.173818516285048, -0.0585031143296301,
0.125084378608705, 0.0655074180474436, 0.254339734692359, 0.00114212078410835
)), class = "data.frame", .Names = c("predictor", "comp_id",
"value"), row.names = c(NA, -140L))
Here is an approach using tidyverse and continuous scale
library(tidyverse)
df %>%
arrange(comp_id, desc(value)) %>% #arrange by comp_id and descending value
mutate(ord = 1:n()) -> dat #create the x scale
ggplot(dat, aes(x = ord, y = value , group = comp_id , colour = comp_id))+
geom_line()+
facet_wrap(~comp_id, ncol = 1, scales = "free_x", drop = TRUE)+
theme(axis.text.x=element_text(angle=35, vjust=1, hjust=1)) +
scale_x_continuous(labels = dat$predictor, breaks = dat$ord, expand = c(0.02, 0.02))
In addition to the nice answer by #missuse, there was another way that gave me what I wanted.
using as factor / as numeric / as.character with the x axis
aes(x = as.factor(as.numeric(as.character(ord)))
and using as numeric /as character while replacing the x axis labels
as.numeric(as.character(ord))
The final script is
ggplot(dat, aes(x = as.factor(as.numeric(as.character(ord))), y = value , group = comp_id , colour = comp_id))+
geom_line()+
facet_wrap(~comp_id, ncol = 1, scales = "free_x", labeller = label_parsed, drop = TRUE)+
theme(axis.text.x=element_text(angle=35, vjust=1, hjust=1,
))+
scale_x_discrete(labels = dat[, setNames(as.character(predictor), as.numeric(as.character(ord)))])

How to use facet_grid correctly in ggplot2?

I'm trying to generate one chart per profile with the following code, but I keep getting "At least one layer must contain all variables used for facetting." errors. I spent the last few hours trying to make it work but I couldn't.
I believe the anwser must be simple, can anyone help?
d = structure(list(category = structure(c(2L, 2L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L,
3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L), .Label = c("4X4",
"HATCH", "SEDAN"), class = "factor"), profile = structure(c(1L,
1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,
1L), .Label = c("FIXED", "FREE", "MOBILE"), class = "factor"),
value = c(6440.32, 6287.22, 9324, 7532, 7287.63, 6827.27,
6880.48, 7795.15, 7042.51, 2708.41, 1373.69, 6742.87, 7692.65,
7692.65, 8116.56, 7692.65, 7692.65, 7692.65, 7962.65, 8116.56,
5691.12, 2434, 8343, 7727.73, 7692.65, 7721.15, 1944.38,
6044.23, 8633.65, 7692.65, 7692.65, 8151.65, 7692.65, 7692.65,
2708.41, 3271.45, 3333.82, 1257.48, 6223.13, 7692.65, 6955.46,
7115.46, 7115.46, 7115.46, 7115.46, 6955.46, 7615.46, 2621.21,
2621.21, 445.61)), .Names = c("category", "profile", "value"
), class = "data.frame", row.names = c(NA, -50L))
library(ggplot2)
p = ggplot(d, aes(x=d$value, fill=d$category)) + geom_density(alpha=.3)
p + facet_grid(d$profile ~ .)
Your problem comes from referring to variables explicitly (i.e. d$profile), not with respect to the data argument in the call to ggplot. There is no need for d$ anywhere.
When faceting using facet_grid or facet_wrap, you need to do so. It is also good practice to do in calls to aes
p <- ggplot(d, aes(x = value, fill = category)) + geom_density(alpha = .3)
p + facet_grid(profile ~ .)

Automatically adjusting ylim with stat_summary

ggplot2 adjust the ylim automatically for the data points. Is there any way to adjust the ylim for stat_summary too?
df <- structure(list(Varieties = structure(c(2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L,
4L, 1L, 2L, 3L, 4L, 1L), .Label = c("F9917", "Hegari", "JS263",
"JS2002"), class = "factor"), Priming = structure(c(2L, 2L, 2L,
2L, 5L, 5L, 5L, 5L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L, 4L, 4L, 4L,
4L, 2L, 2L, 2L, 2L, 5L, 5L, 5L, 5L, 3L, 3L, 3L, 3L, 1L, 1L, 1L,
1L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 5L, 5L, 5L, 5L, 3L, 3L, 3L,
3L, 1L, 1L, 1L, 1L, 4L, 4L, 4L, 4L), .Label = c("CaCl2", "Dry",
"Hydropriming", "KNO3", "OnFarmpriming"), class = "factor"),
PH = c(225.8, 224.26, 228.9, 215.82, 230.3, 227.7, 232.8,
221.1, 260.2, 230.8, 236.75, 230.5, 250.56, 230.74, 240.64,
226.7, 268.4, 233.4, 243.33, 232.7, 252.04, 233.1, 237.14,
220.6, 265.55, 234.93, 240.04, 218.21, 300.55, 245, 243.5,
234.65, 253.3, 233.5, 238.62, 225.93, 255.74, 233.64, 238.1,
230.93, 246, 240.33, 246.08, 221.7, 250.54, 242.87, 251,
225.32, 251.47, 245.4, 266.74, 227.73, 290.62, 246.68, 256.4,
225.83, 282.67, 240.58, 258.35, 235.87)), .Names = c("Varieties",
"Priming", "PH"), class = "data.frame", row.names = c(NA, 60L
))
p1 <- ggplot(data=df, aes(x=Varieties, y=PH, group=Priming, shape=Priming, colour=Priming))+
stat_summary(fun.y=mean, geom="point", size=2, aes(group=Priming, shape=Priming, colour=Priming))+
theme_bw()
p1 <- p1 + stat_summary(fun.y=mean, geom="line", aes(group=Priming, shape=Priming, colour=Priming))
print(p1)
See extra space in ylim for stat_summary values. Thanks in advance for your help and time.
Here is one approach, using plyr to prep the data before plotting
df <- ddply(df, .(Varieties, Priming), transform, meanPH = mean(PH))
ggplot(df, aes(Varieties, meanPH)) +
geom_point() +
geom_line(aes(group = Priming, color = Priming))
The current "official" answer for 0.8.9 is, I believe, that you can't, at least not automatically, and not without preprocessing the data as Ramnath indicates. Most people asking this question, or some variant of it, are pointed towards setting the limits manually using coord_cartesian.
The reason stat_summary behaves this way is that it sort of assumes that you aren't going to just plot the summaries, but at least some of the underlying data as well, so it sets up the plotting area using the underlying data frame.
However, I found this thread on the ggplot2 list that suggests this behavior might change in the upcoming 0.9.0 release. (The thread is a little vague, but I read it as implying that in the next version, if the only layer you add is form stat_summary then the plot limits will be calculated based on the summaries, not the original data. I could be wrong though.)

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