search for: scale_y_log10

Dear ggplot2 users, is there an easy/elegant way to suppress zero count bars in histograms with logarithmic y axis ? One (made up) example would be qplot(exp(rnorm(1000))) + geom_histogram(colour = "cornsilk", fill = "darkblue") + scale_x_sqrt() + scale_y_log10() Thanks! Markus [[alternative HTML version deleted]]

...system.time requires a explicit print, but it's on the order of a few seconds). I'm not sure if I've provided enough information to be able to solve the problem, so please let me know what additional details would be useful. Thanks, Hadley > ggplot(mtcars, aes(x=cyl, y=-mpg)) + scale_y_log10() + geom_point() Error in grid.pretty(.$domain()) : infinite axis extents [GEPretty(-inf,inf,5)] In addition: Warning messages: 1: NaNs produced in: log(x, base) 2: no non-missing arguments to min; returning Inf 3: no non-missing arguments to max; returning -Inf 4: no non-missing arguments to min;...

...function (X) { d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE) png(paste("img/", X, ".png", sep="")) ggplot(d, aes(x=condition, y=count, color=condition)) + geom_point(position=position_jitter(w=0.1,h=0)) + scale_y_log10(breaks=c(25,100,400)) + ggtitle(X) + theme(plot.title = element_text(hjust = 0.5)) dev.off() } 'd' is a dataframe count condition E11.5 F20HET BA40_quant 955.9788 E11.5 F20HET E11.5 F20HET BA45_quant 796.2863 E11.5 F20HET...

...Counts(dds2, gene=X, intgroup="condition", returnData=TRUE) >> png(paste("img/", X, ".png", sep="")) >> ggplot(d, aes(x=condition, y=count, color=condition)) + >> geom_point(position=position_jitter(w=0.1,h=0)) + >> scale_y_log10(breaks=c(25,100,400)) + >> ggtitle(X) + >> theme(plot.title = element_text(hjust = 0.5)) >> >> dev.off() >> } >> >> 'd' is a dataframe >> >> count condition >> E11.5 F20HET BA40_...

...d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE) > png(paste("img/", X, ".png", sep="")) > ggplot(d, aes(x=condition, y=count, color=condition)) + > geom_point(position=position_jitter(w=0.1,h=0)) + > scale_y_log10(breaks=c(25,100,400)) + > ggtitle(X) + > theme(plot.title = element_text(hjust = 0.5)) > > dev.off() > } > > 'd' is a dataframe > > count condition > E11.5 F20HET BA40_quant 955.9788 E11.5 F20HET >...

...") #Removes the NAs MyDataWONA <- MyData[!is.na(MyData$Detections), ] #does the plot p <- ggplot(data = MyDataWONA, aes(x=Year, y=GW_Elv , col=Detections)) + geom_point(aes(shape=Detections)) + ##sets the colors scale_colour_manual(values=c("black","red")) + #scale_y_log10() + #location of the legend theme(legend.position=c("right")) + #sets the line color, type and size geom_line(colour="black", linetype="dotted", size=0.5) + ylab("Elevation Feet Mean Sea Level") ## does the graph using the Location IDs as the dif...

...+geom_line(data=d,aes(x=d[["x"]],y=d[["y1"]]),colour="blue") p<-p+geom_line(data=d,aes(x=d[["x"]],y=d[["y2"]]),colour="red") p2+scale_y_continuous() ...gives the plot I want, only with my actual data, I'd need it in log-scale: p2+scale_y_log10() shifts the ribbon far above the actual data (factor 1000, if I see it right, but I haven't tested it with different data to check on that...). I'm using the latest version of ggplot2 (0.5.7). Has anyone any suggestions for a workaround/patch? Many Thanks, Martin

Hello, I generate box plots from my data like this: qplot(x=xxx,y=column,data=data,geom="boxplot") + xlab("xxx") + ylab(ylabel) + theme_bw() + scale_y_log10() + geom_jitter(alpha=I(1/10)) The problem is that I see lot of points above the maximum at the same level as some outliers. It looks very weird as I expected the outliers to be "few" and specially not see any points other than the outliers below the minimum or above the maximum indicato...

...lotting the first graph. library(ggplot2) df <- data.frame(x = rep(1:10, 10), y = rnorm(100)) df$y <- 10 ^ (df$x + df$y) df <- cbind(df, predict(lm(I(log10(y)) ~ x, data = df), interval = "c")) df[, 3:5] <- 10 ^ df[, 3:5] ggplot(data = df, aes(x = x, y = y)) + geom_point() + scale_y_log10() + geom_line(aes(y = fit)) + geom_errorbar(aes(min = lwr, max = upr)) ggplot(data = df, aes(x = x, y = y)) + geom_point() + scale_y_log10() + geom_line(aes(y = fit)) + geom_errorbar(aes(min = log10(lwr), max = log10(upr))) Thanks, Thierry -------------------------------------------------------...

Hi, Does anyone know how to do a coord_trans() in which the y-axis is tranformed into (for example) -1000/y? Thanks, _____________________________ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011

...A <- MyData[!is.na(MyData$Detections), ] > > #does the plot > p <- ggplot(data = MyDataWONA, aes(x=Year, y=GW_Elv , col=Detections)) + > geom_point(aes(shape=Detections)) + > > ##sets the colors > scale_colour_manual(values=c("black","red")) + #scale_y_log10() + > > #location of the legend > theme(legend.position=c("right")) + > > #sets the line color, type and size > geom_line(colour="black", linetype="dotted", size=0.5) + > ylab("Elevation Feet Mean Sea Level") > > ## doe...

...quot;NonDetect") #does the plot p <- ggplot(data = MyData, aes(x=Year, y=Chloride , col=Detections)) + geom_point(aes(shape=Detections)) + #sets the detect vs. non-detect colors scale_colour_manual(values=c("black","red")) + #sets the y scale and log base 10 scale_y_log10() + ##adds line geom_hline(aes(yintercept=250),linetype="dashed")+ #location of the legend theme(legend.position=c("right")) + #sets the line color, type and size geom_line(colour="black", linetype="dotted", size=0.5) + ylab("Chloride (m...

...t fecal coliform plot yfc_plot<-ggplot(yfc) + geom_boxplot() + aes(x=as.factor(year2), y=fc) + opts(axis.text.x=theme_text(angle=45, hjust=1, vjust=1)) + xlab(" \n Date") + ylab("Fecal coliforms (cfu/100 mL) \n ") + geom_smooth(stat='smooth', aes(group=1), size=1.5) + scale_y_log10() #arrange plots together grid.arrange(yp_plot, yfc_plot, ncol=1) You can see that I got the plot areas to line up using grid.arrange(), but the x-axes are still off. I'd really appreciate any help I can get. Thanks, Saalem [[alternative HTML version deleted]]

...otp <- ggplot(data = MyData, aes(x=Year, y=Chloride, col=Detections)) +? geom_point(aes(shape=Detections)) +? geom_line(data = MyData,aes(y=SMCL))+?? ?#sets the detect vs. non-detect colors? scale_colour_manual(values=c("black","red")) +???? #sets the y scale and log base 10? scale_y_log10() +??? #location of the legend??? theme(legend.position=c("right")) +??? #sets the line color, type and size? geom_line(colour="black", linetype="dotted", size=0.5) +? ? ylab("Chloride (mg/L)") ## does the graph using the Location IDs as the different Locatio...

...ariable don't exist in the environment calling the function.. e.g: my function does something like: getPlot<-function(da=NULL,...){ #1st column holds x-values, others hold data series to plot... co<-as.character(names(da)) co<-co[2:length(co)] pl<-ggplot(data=da) pl<-pl+scale_y_log10()+scale_x_continuous() for(c in co){ pl<-pl+geom_line(x=da[[1]],y=da[[c]],mapping=aes(x=da[[1]],y=da[[c]])) } return(pl) } I need to add every layer separately, because I want to be able to explicitly define attributes for every data series (colour, size... e.g. highlight only two speci...

Dear All, I would like to be able to plot histograms/densities on a semi-log or log-log scale. I found several suggestions online http://tolstoy.newcastle.edu.au/R/help/05/09/12044.html https://stat.ethz.ch/pipermail/r-help/2002-June/022295.html http://www.harding.edu/fmccown/R/#histograms Now, consider the code snippet taken from http://www.harding.edu/fmccown/R/#histograms # Get a random

...s my attempt : library(ggplot2) x<-1:10 y<-x^2 df<-data.frame(x=x,y=y) p1<-ggplot(df,aes(x,y))+geom_point()+ scale_x_log10( breaks = scales::trans_breaks("log10", function(x) 10^x), labels = scales::trans_format("log10", scales::math_format(10^.x)) ) + scale_y_log10( breaks = scales::trans_breaks("log10", function(x) 10^x), labels = scales::trans_format("log10", scales::math_format(10^.x)) ) +theme_bw() p2<-p1 + annotation_logticks() p2 p2 + scale_y_continuous(sec.axis = sec_axis(~.)) I get the following error : Scale for ...

Dear all, I would like to generate a filled.contour plot with log x and y axis, however using: filled.contour(as.line,log="xy") results in a warning message. Does anybody knos what to do? Thanks Thomas

My question is related to plot( ) in the mgcv package. Before modelling the data, a few predictors were transformed to normalize them. Therefore, the x-axes in the plots show transformed predictor values. How do I back-transform the predictors so that the plots are easier to interpret? Thanks in advance, Suzan -- Suzan Pool Oregon State University Cooperative Institute for Marine

...quot;NonDetect") #does the plot p <- ggplot(data = MyData, aes(x=Year, y=Chloride , col=Detections)) + ? geom_point(aes(shape=Detections)) + ? #sets the detect vs. non-detect colors ? scale_colour_manual(values=c("black","red")) + ? #sets the y scale and log base 10 ? scale_y_log10() + ? ##adds line ? geom_hline(aes(yintercept=250),linetype="dashed")+ ? #location of the legend ? theme(legend.position=c("right")) + ? #sets the line color, type and size ? geom_line(colour="black", linetype="dotted", size=0.5) + ? ylab("Chloride (m...