Changelog

Source: NEWS.md

qntmap 1.0.2

Bug fix

  • Fix qntmap() raising error on the Mapping conditions pane of the Input page, “Can’t create column Values: Can’t combine ..1 and ..2 ” (#34).

  • Fix cluster_xmap() raising error when checking unit of pixels (#36)

Internal changes

  • Use GitHub Actions for CI (#35)
  • Updated tests and DESCRIPTION to pass CI (#37)

qntmap 1.0.1

  • Phase list csv can be without id column.
  • Reorder summarized tables in the shiny GUI.
  • autoplot.qm_xmap() supports data with unknown step size.

Bug fix

  • Fix beta being wrong in the Params for Quantify page.

Planning

  • Add remove_outliers option to quantify and find_centers

qntmap 1.0.0

Biggest NEWS

  • Graphical user interface is ready! Run qntmap() to enjoy it.

Breaking changes

  • qntmap() default to use shiny web app. Specify shiny = FALSE to use legacy console-based intearactive mode. Note that the legacy one is no more maintained.
  • read_qnt()
    • omits the renew option
    • uses the saving option only to save phase list, no more to cache data
  • read_xmap()
    • omits the saving and the renew option
    • returns a data frame with columns x and y indicating coordinates of pixels instead of a list
  • cluster_xmap()
    • returns a data frame with the center attribute unlike older one returned a list
    • omits group_cluster option. Instead, apply group_subclusters() to the result to integrate subclusters.
    • saves the result
      • as is in the formats of RDS, png (dot-by-dot phase map), and svg (phase map with legend)
      • converted by group_subclusters in the format of only png and svg
  • group_subclusters()
  • pick() changed its first argument to .df from .data.
  • The magma color scale become the default one to plot of mapping data instead of the viridis.
  • Use message rather than cat so that they can be suppressed by users.

Major changes and new features

  • autoplot() methods are implemented to follow the best practice of ggplot2. From now on, plot() methods are wrappers of autoplot.
  • find_outlier() is implemented to detect outliers cause mainly by mapping fine grained phases.
  • find_outlier() is implemented to detect unexpectedly high or low mapping intensities compared to spot intenstieis, which typically occurs due to outliers are analysing multi-phase pixels
  • find_centers()
    • has more robust approach to find centroids powered by find_outlier()
    • has additional arguments
      • phase and element: Specifying them controls which phases and elements are used to find outliers. They suppot tidyeval. For example element = c(Si, Ti, Al) indicates the 3 elements are used, and element = c(-Si, -Ti, -Al) indicates the 3 elements are NOT used.
      • epma: If tidy_epma is already performed, then specify the result here to save time.
    • deprecates fine_phase which is generalized by phase.
  • tidy_epma has new arguments subcluster and suffix.
  • hmean() and vmean() supports the objects with class qntmap, qm_xmap, and qm_cluster.mPreviously they only supported the qntmap class object.
  • All layers for ggplot2 are no longer pre-compiled at installation stage. This is to avoid possible conflicts on updates on ggplot2 after installing qntmap.
  • quantify() get the params attribute showing the parameters, alpha, beta, and gamma.
  • autoplot.qm_epma() is defined for the result of tidy_epma()

Internal changes

  • tidy_epma() returns qm_epma class object.
  • gghist.numeric()
    • draws border to be legible regardless of background colors.
    • supports a histogram with a single column.
  • correct_deadtime() supports re-calculation of dead time.
  • prioritize() accepts unnamed vector.
  • save4qm() methods, summary() methods, pick(), mean(), vmean(), and hmean() are re-written to support new data structures.
  • correct_deadtime() is factored out from read_xmap(), but not exported currently.
  • Themes for plot supports modifying base_size, so that the appearance can be optimized in Shiny App.
  • Full support of tidyeval
  • Tidyverse and r-lib related functions are imported in qntmap-package.R to avoid importing the same funcions in multiple files.
  • Tests run faster by exporting duplicated codes to setup.R.

qntmap 0.3.4

New features

Major changes

  • Drastically improved performance of plot()
  • Clustering results will be saved as an RDS file, a dot-by-dot png image without legend, and a ggplot2 plot with legend saved as svg.
    • The size of ggplot2 plot is set to A4 (297 mm * 420 mm), either horizontal or vertical which fits best to the plot.
    • The legend used to be saved as a pie chart.

qntmap 0.3.3

Breaking changes

  • quantify() no more calculates standard errors by default. This is to save time and memory usage. Set se = TRUE to calculate the errors.
  • Format of “params.csv” created by quantify() is changed.
    • Column “elem” is renamed to “oxide”
    • Column “elint” is renamed to “element”
    • Columns "*_se" are removed.

New features

  • quantify() and tidy_epma() supports maps and spots analyzing inequal elements.

    Example Mapped elements Spot elements
    A Si, Ti, Mg Si, Mg
    B Si, Mg Si, Ti, Mg
    C Si, Ti, Mg Si, Mg, Ca

Bug fix

  • Calculation of standard errors for compositions of pixels were wrong.

qntmap 0.3.2

Major changes

  • quantify() saves parameters alpha, beta, gamma, and their standard errors when saving = TRUE.
  • quantify() loads parameters from a csv file by giving its path to fix parameter.
  • read_qnt() and read_xmap() supports to retrieve analytical conditions from manually prepared csv files. This feature is implemented to avoid failures in reading data caused by difference in formats output by different EPMA instruments.
  • Hover on plot() of mapping data shows coordinates and a chemical composition of a selected element.

qntmap 0.3.1

Major changes

  • quantify() supports fixing compositions of certain components of phases.
  • Defunct deprecated functions:
    • qltmap_cls_centers
    • qltmap_load
    • qnt_load
    • qntmap_cls_pois
    • qntmap_quantify
  • Support for searching online documents: https://qntmap.atusy.net

Minor changes

  • Refactored to
    • simplify codes
    • separate monster functions into small ones
  • Introduced continuous integrations:
    • Travis CI, AppVeyor, and Codecov
    • As Travis CI passes building on macOS, #23 is closed.

Decisions

  • qntmap() will be maintained without new features to focus on developing web user interface with shiny package.

qntmap 0.3.0

Major changes

  • plot()
    • Interactive plot is a combination of shiny, ggplot2, and more. No more using plotly.
      • Color control with histogram
      • Hover information of pixels
      • Zooming
      • Moving
      • Summarizing data in a table below heatmap
        • Double click to keep pixel data
        • Box select to keep mean values of data
    • Grayscale is supported in addition to viridis. #28
    • Clustering result is supported. #28
  • segment()
    • Only allows PNG format as an input. No more JPG nor BMP allowed.
    • Independent from imager package. #16

qntmap 0.2.2

Major changes

New features

  • read_xmap()
    • It checks version of QntMap which created former version of xmap.RDS in case renew = FALSE
    • It’s returning value has following attributes:
      • deadtime: deadtime specified by a parameter DT
      • dir_map: path of the directory which contains raw data
      • dwell: dwell time
      • current: probe current
      • start: mapping starting position
      • pixel: size of mapping area
      • step: step size of pixels
      • ver: version of qntmap package
      • instrument: version of EPMA
      • class: c('qm_xmap', 'list')
  • plot
  • plot_shiny
    • alos uses viridis color scale
    • limits hover info for performance improvement

Minor changes

  • read_cnd, read_map_pos, and read_map_beam are no more in use but are remained for awhile. Note they are not exported functions.

qntmap 0.2.1

New features

qntmap 0.2.0

Check NEWS as 0.2.0 have lots of breaking changes.

Breaking changes

  • Renamed functions to follow verb_hoge style. This leads some functions to be deprecated or defunct. See “Summary of defunct, deprecated, and unexported functions”.
  • Unexported cipois and flag0.
  • Renamed arguments to be shorter and easy-remembering.
  • Reduced arguments which are reused again and again by utiliing attributes. For example,
    • Path to the directory containing X-ray map data is specified by dir_map or wd in use of epma_tidy, qltmap_cls_centers, qltmap_cls_pois, qltmap_load, and so on. However, now is only specified in read_xmap.
  • The above change cause read_qnt to save its result (qnt.RDS) and semi-product (phase_list0.csv) in the directory containing .qnt files unlike qnt_load saved them under the working directory.

Major changes

  • Monster functions are separated into smaller functions.
    • A wrapper part of PoiClaClu::Classify in cluster_xmap (formerly qltmap_cls_pois) is isolated as cluster
    • Internal parameters for quantify are calculated using find_AB, find_AG, and find_B
    • Codes for saving result of functions are isolated as S3 generics of save4qm.
  • Condition files of EPMA analysis are read by S3 generics to support various types of file formats.
  • find_centers (former qltmap_cls_centers) become more robust against multi-phase pixels by - finding pixels analyzing multi-phase pixels by comaring with corresponding quantified points. - predicting X-ray map counts of a target phase in multi-phase pixels based on regression analysis.
  • cluster_xmap does not group_clusters by default.

Minor changes

  • Performance improvements by simplifying codes, utilizing matrixStats package, and so on.
  • quantify supports fixing internal parameters (A and B).

Summary of defunct, deprecated, and unexported functions

old (0.1.0) new (0.2.0) condition of old
cipois cipois unexported
epma_tidy tidy_epma defunct
flag0 flag0 unexported
qltmap_cls_centers find_centers deprecated
qltmap_cls_centers_random find_centers_kpp defunct
qltmap_cls_pois cluster_xmap deprecated
qltmap_cls_pois_integrate group_clusters defunct
qltmap_load read_xmap deprecated
qnt_load read_qnt deprecated
qntmap_quantify quantify deprecated