Point shape in ggplot2 with distance matrix

[Roxane]

Hello Rstudio community,
I have just a little problem when I create a PCoA representation with ggplot2 (representation joint) . I used a matrix distances (with Bray Curtis) but I need a shape differentiation by size in my samples ( 0.2 and 3) in addition with the differentiation by color for origin sample (need four colors Laz, Mis, QN, Sur). Do you think there are a solution for these in ggplot2 with a matrix distances ?
Thank you for your help

[andresrcs]

Could you ask this with a minimal REPRoducible EXample (reprex)? A reprex makes it much easier for others to understand your issue and figure out how to help.

FAQ: What's a reproducible example (`reprex`) and how do I create one?

Why reprex? Getting unstuck is hard. Your first step here is usually to create a reprex, or reproducible example. The goal of a reprex is to package your code, and information about your problem so that others can run it and feel your pain. Then, hopefully, folks can more easily provide a solution. What's in a Reproducible Example? Parts of a reproducible example: background information - Describe what you are trying to do. What have you already done? complete set up - include any library() calls and data to reproduce your issue. data for a reprex: Here's a discussion on setting up data for a reprex make it run - include the minimal code required to reproduce your error on the data…

[Roxane]

Sorry , I ask some help on R community for the first time.
May be with the code like these it's better :

#Load library
library("ggplot2")
library("scales")
library("grid")
library("reshape2")
library("plotly")
library("reshape2")
library("vegan")
library("vegetarian")
library("factoextra")
library("HH")
library("usdm")
library("stats")
library("ggfortify")
library("cluster")
library("ecodist")

#Make a csv table very simple, with letter instead of name in row and columns 
data("iris")
#import data
datamatrix<-distance(iris[, 1:4], "bray-curtis")

#Check data
#View(datamatrix)
#Bray-curtis distance
dist <- distance(datamatrix, method="bray-curtis")
matrixdist <- as.matrix(dist)

#Use a distance matrix for applicate this code 
#Charger la librairie nécessaire
library("ggplot2")
library("scales")
library("grid")
library("reshape2")
library("plotly")
library("reshape2")


pcoA<-read.table(file="matrixbc.txt", header=T, sep="\t", dec=",")
#pcoA

palette=c("#99cc00", "#33ff33", "#ffcc00","#ffff00","#ff33cc","#ff3399","#ff3300","#990000")
names(pcoA)[2:3] <- c('pcoA1', 'pcoA2')

ggplot(pcoA, aes(x=pcoA1 , y = pcoA2), shape= size) + #but where I have my problem
  theme_bw() +
  geom_point(aes(colour=1), size =3, pch=19) +
  scale_colour_manual('Species',values=palette)

[andresrcs]

@Roxane

pcoA<-read.table(file="matrixbc.txt", header=T, sep="\t", dec=",")

Sorry but your code is not actually reproducible since we don't have access to "matrixbc.txt" file, and it's not pretty clear what you want to achieve, could you elaborate a little more in your question? Also, please narrow down your code to just the relevant section (only include the libraries relevant to your issue).

Maybe this FAQ would give you a better idea of how to make a proper reprex

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…