In atusy/qntmap: Enhance quantitative analysis of EPMA map

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(ggplot2)
library(dplyr)
library(knitr)
library(qntmap)

Introduction

This document introduces a way to quantify X-ray maps without quantitatively analyzed spots by inheriting parameters from a previously quantified X-ray map (See figure below).

set.seed(1)
spots <- runif(40) %>%
  matrix(ncol = 2, dimnames = list(NULL, c("x", "y"))) %>%
  as.data.frame
rect <- data.frame(xmin = c(0, 3), xmax = c(1, 4), ymin = 0, ymax = 1)

ggplot(spots) +
  geom_rect(aes(xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax), data = rect) +
  geom_point(aes(x, y)) +
  annotate("text", x = 2, y = -Inf, label = "Sample", vjust = -1, size = 8) +
  annotate("text", x = c(0.5, 3.5), y = 1, vjust = -.3, size = 5, label = c(
    "(a) Mapped area\nwith spots",
    "(b) Mapped area\nwithout spots"
  )) +
  xlim(-1, 5) +
  ylim(-1.5, 2.5) +
  theme(
    axis.ticks=element_blank(),
    axis.ticks.length=unit(0, "null"),
    axis.text=element_blank(),
    axis.title=element_blank(),
    axis.line=element_blank(),
    panel.background=element_rect(fill = "gray",colour = NA),
    panel.border=element_blank(),
    panel.grid=element_blank(),
    panel.spacing=unit(c(0,0,0,0), "null"),
    plot.margin=unit(c(0,0,0,0), "null"),
    legend.position="none",
    legend.margin=margin(0,0,0,0, "null"),
    NULL
  ) +
  NULL

Requirements

• qntmap 0.3.2 or later
• Referencial quantified maps from a single area.
  • The maps must be constructed by quantify(saving = TRUE) under qntmap 0.3.2 or later.
  • To construct a referencial maps, read "Get started".
• X-ray maps to be quantified.
  • The new maps must be analyzed under the same conditions to the reference maps.
  • The new maps must comprise mineral assemblage which is a subset of the reference maps.

Instructions

Load qntmap package

library(qntmap)

Read X-ray mapping data to be quantified

xmap <- read_xmap(".map/2 for example")

Cluster analysis

Initialize cluster centers

Suppose available quantified maps are constructed by following "Get started", centers_initial0.csv is available as well. Read the csv file by following codes.

centers <- read.csv("example/centers_initial0.csv")
centers

dirs <- file.path(system.file('extdata', 'minimal', package = 'qntmap'), c(".map/1", ".qnt"))
xmap <- read_xmap(dirs[[1]])
qnt <- read_qnt(dirs[[2]], saving = FALSE)
kable(find_centers(xmap, qnt, saveas = FALSE))

The above is a example format of initial centers given by sample data introduced in "Get started". Edit the csv file manually if initial centers require modifications, or if there are any phase abscent in new maps to be quantified.

Run cluster analysis

cluster <- cluster_xmap(xmap, centers)

Quantification

When available quantified mapes are compsoed by quantify() function, parameters.csv is saved in the qntmap directory within the directory storing X-ray mapping data. Specify a file path of parameters.csv as fix parameter of quantify() function.

quantify(xmap = xmap, qnt = NULL, cluster = cluster, fix = "example/qntmap/parameters.csv")

Note that qnt paramter is ignored when fix parameter is specified.

atusy/qntmap documentation built on April 11, 2021, 4:45 p.m.