Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.

. • `•. .• `•. .><º>`•. . • `•. .• >`•. .><º> Anna Zakrisson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden/Sverige Lives in Berlin. For paper mail: Katzbachstr. 21

Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.

"ATCGCGCGAATA"))) # I am very grateful for your help! I am no whiz at R and everything I know # is self-taught. Therefore, some basics can turn out to be quite some # obsatcles for me. # /Anna ><º>`•. . • `•. .• `•. . ><º>`

[R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data.

erA = factor(rep(LETTERS[1:2], each = 5)), B1298712 = factor(rep(LETTERS[1:2], each = 5))) # Many thank's and with kind regards Anna Zakrisson ><�>`�. . � `�. .� `�. . ><�>`�. . � `�. .� `�. .><�>`�. . � `�. .� >`�. .><�> Anna Zakr

[R] lattice, latticeExtra: Adding moving averages to double y plot

in insering this into lattice (I am not an experienced lattice user). I want to keep the data points in the plot. Find below dummy data and the script as well as annotations further describing my question. thank you in advance! Anna Zakrisson mydata<- data.frame( Year = 1980:2009, T

[R] ggplot2: removing empty factor levels in facet_grid

theme_bw() + theme(strip.background = element_blank()) + ggtitle("this plot is ugly but ignore that")+ xlab("my x-axis stuff")+ ylab("my y-axis stuff")+ theme(legend.title=element_blank(), legend.key = element_blank()) p Anna Zakrisson Braeunlich PhD stude

[R] ggplot2: how to add new names to legend

tle.x = element_text(size=10, colour="black", family="serif", angle=00))+ theme(axis.title.y = element_text(size=10, colour="black", family="serif", angle=90)) p p1 <- p+theme(legend.title=element_blank()) p1 p2 <- p1+ theme(legend.key = element_blank(

[R] ggplot2: geom_boxplot. Mapping aes factor but with different color scale and hatching

t;N")))+ xlab("Station") + scale_shape(solid = FALSE)+ geom_hline(yintercept=0, linetype=3)+ scale_fill_discrete(guide = guide_legend("my stuff"), labels=c("cyanobacteria", "seston")) #if I wanted to have "seston" in italic

[R] saving as TIFF - problem with compression

columns=1, border=F, x = 0.2, y = 0.2, corner = c(2, 2), title="", cex.title=1.3), ylab = ("Pc"), xlab="Week", data= SummPdata,type="o",

[R] lattice: double y - problem changing axis color after doubleYScale

tP doubleYScale(plotN, plotP, add.ylab2 = TRUE) #Why can I not change the axis color by adding to this argument? # I want the y1 and y2 axes to be defined not by color, but by shape and linetype. # I have managed to draw the shapes (defined by Nc and Pc) by the y1 and y2 axes, but I do not mana

[R] ggplot2: two y-axis - any change?

lattice for every second plot. What are your thoughts on this for the future and are there already some possibilities in place? I prefer continusing using ggplot2 because it is brilliant. with kind regards Anna Zakrisson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences

[R] ggplot2: changing strip text in facet_grid and a legend text problem

colour="black", family="serif", angle=00)) + theme(strip.text.y = element_text(size = 16, colour="black", family="serif", angle=00)) + theme(axis.text.x = element_text(size = 16, colour="black", family="serif", angle=00)) + theme(axis.text.y

[R] ggplot2: changing shapes facet_grid - special case.

eme(axis.text.x = element_text(size = 20, colour="black", family="serif", angle=00)) + theme(axis.text.y = element_text(size = 17, colour="black", family="serif", angle=00)) + theme(axis.title.x = element_text(size=20, colour="black", f

Re: [R] ggplot2: connecting medians of boxes using facet_wrap. Changing median marker.

t;summary", fun.y = "median", mapping=aes(shape=organism)) + #must be unfilled theme(strip.text.x = element_text(size = 12, colour="black", family="serif", angle=00)) + theme(axis.text.x = element_text(size = 12, colour="black", family="serif", angle=90)) + theme(axis.text.y

[R] ggplot2: connecting medians of boxes using facet_wrap. Changing median marker.

gle=90)) + theme(axis.text.y = element_text(size = 12, colour="black", family="serif", angle=00)) + geom_hline(yintercept=0, linetype=3) #draws dotted line at 0 p # method="lm" is definately wrong, # I just added it to be a ble to draw some lines at all. # I

Re: [R] lattice: bwplot: getting two plots into one.

.settings), key=list(text=list(c("factor2a","factor2b", "factor2c"), col="black"), points=list(pch=rep(2:4), cex=1, col="black"), x = .35, y = 1.06, corner = c(2, 2)), #legend p

Re: [R] lattice: bwplot: getting two plots into one.

:3), panel=panel.bwplot.intermediate.hh, key=list(text=list(c("factor2a","factor2b", "factor2c"), col=c("black")), space="right", points=list(pch=c(1:3), lty=c(1,3), cex=1, col=c("

Re: [R] lattice: bwplot: getting two plots into one.

on top of each other - again, this will look terribel on this data, but will be OK for mine. Is this possible in lattice? Maybe using different data frames and make different plots and superpose them on top of each other? Ideas? ggplot2? with kind regards Anna Zakrisson Braeunlich PhD student Dep

[R] lattice: bwplot: getting two plots into one.

sson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden/Sverige Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, Berlin - Kreuzberg Germany/Deutschland E-mai

Re: [R] Lattice: bwplot - changing box colors in legend and plot when using panel.groups = function... and panel = panel.superpose

t;gray","white")), # boxplots #superpose.fill=list(col=c("black","white")), superpose.polygon=list(col=c("gray","white")), # legend par.sub=font.settings) as adviced by you. With kind regards Anna Zakrisson Braeunlich PhD student Depa

[R] Lattice: bwplot - changing box colors in legend and plot when using panel.groups = function... and panel = panel.superpose

panel.groups = function(x, y, ..., group.number) { panel.bwplot(x + (group.number-1.8)/3, y, ...) }) Anna Zakrisson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden/Sverige Lives

Re: [R] ggpliot2: reordering of factors in facets facet.grid(). Reordering of factor on x-axis no problem.

again, thank you so much! Another day closer to disputation... :-S Anna Anna Zakrisson Braeunlich PhD student Department of Ecology Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, B

Re: [R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

GREAT! Thank you! Will try this! Anna Anna Zakrisson Braeunlich PhD student Department of Ecology Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, Berlin - Kreuzberg Germany

[R] ggpliot2: reordering of factors in facets facet.grid(). Reordering of factor on x-axis no problem.

d of alphabetical. My normal methods do not work. with kind regards Anna Zakrisson # Some dummy data: mydata<- data.frame(factor1 = factor(rep(LETTERS[1:6], each = 80)), factor2 = factor(rep(c(1:5), each = 16)), factor3 = factor(rep(c(1:4), each = 4)),

Re: [R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

FALSE)+ theme_bw() + theme(strip.background = element_blank())+ theme(strip.text.x = element_blank(), strip.text.y = element_blank())+ ylab(expression(paste("my measured stuff"))) + xlab("factor3") + theme(legend.position="none")+ labs(shape = "factor1

Re: [R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

rouping, ncol = 2) + theme(strip.background = element_blank()) + scale_shape(solid = FALSE)+ theme_bw() + ylab(expression(paste("my measured stuff"))) + xlab("factor3") + theme(legend.position="none")+ labs(shape = "factor1", group = "facto

Re: [R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

tweaking grid.arrange. This will come in handy! With kind regards Anna Zakrisson Braeunlich PhD student Department of Ecology Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, Berlin

Re: [R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

Dear Stephen, thank you for the tip regarding Incskape. I had never heard of it before. It looks extremely useful! With kind regards Anna Zakrisson Braeunlich PhD student Department of Ecology Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden

Re: [R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

problem. I also found: theme(legend.justification=c(1,0), legend.position=c(1,0)) for the legend justification. Now this starts to look like how I want it to! Thank you so much for your time! Best regards Anna Zakrisson Braeunlich PhD student Department of Ecology Environment and Plant Sciences

[R] Ggplot2: Moving legend, change fill and removal of space between plots when using grid.arrange() possible use of facet_grid?

;white", #Why is the fill commando not working? position = "dodge", width = 0.3, size=3) + geom_line(aes(linetype=factor1), color = "black", size = 0.5) + geom_errorbar(aes(ymin = mean - sdv , ymax = mean + sdv), width = 0.3, position = "d

[R] How to plot 2 continous variables on double y-axis with 2 factors: ggplot2, gplot, lattice, sciplot?

ing this in ggplot2? I have also tried plotmeans() in the sciplot package, but was unsuccessful. Sincerely Anna Zakrisson library(plotrix) ?brkdn.plot par(family="serif",font=1) brkdn.plot("y1", "factor1","factor2", data=mydata, mct="mean&

[R] introducing jitter in overlapping graphs using ggplots (plotmeans). Also sciplot.

d the standard deviations instead of the default standard errors. Thank you for taking your time. I have spent a long time trying to solve this and the frustration slowly approaches anger (in myself) :-) Yours sincerely Anna Zakrisson Braeunlich PhD Student Department of Systems Ecology S

[R] plotting smoother function on raw data

ase, help me Anna Anna Zakrisson Braeunlich PhD Student Department of Systems Ecology Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm E-mail: a...@ecology.su.se Tel work: +46 (0)8 161103 Mobile: +46-(0)700-525015 Web site: http://www.ecology.su.se/staff/personal.asp?id=163 &

[R] Autocorrelation values? How to extract?

multiply the dependent variable autocorrelation with the independent variable autocorrelation and then multiply by (N-j)/N where N is the sample size and j is the lag...calculate z-value...adjust my p-value...Sincerely Anna Zakrisson Braeunlich PhD Student Department of Systems Ecology Stockholm

[R] corCompSymm in gamm()?

you for your time! Anna Zakrisson Braeunlich PhD Student Department of Systems Ecology Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm E-mail: a...@ecology.su.se Tel work: +46 (0)8 161103 Mobile: +46-(0)700-525015 Web site: http://www.ecology.su.se/staff/personal.asp?id=163 >&

[R] Labels in xy-plots

nt colours/other markings (irrelevant for me) and identified on the side of the graph. Thank's! Anna Zakrisson Braeunlich PhD Student Department of Systems Ecology Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm E-mail: a...@ecology.su.se Tel work: +46 (0)8 161103 Mobile: +4