doc

.Rbuildignore

@@ -1,3 +1,4 @@
+^README\.Rmd$
 ^docs$
 ^_pkgdown\.yml$
 ^.*\.Rproj$

.gitignore

@@ -9,3 +9,5 @@ qntmap.Rproj
 vignettes/center_add\.csv
 
 vignettes/centers0\.csv
+
+vignettes/\.build\.timestamp

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: qntmap
 Type: Package
-Title: Enhance quantitative analysis of EPMA data
-Version: 0.2.2
+Title: Enhance quantitative analysis of EPMA map
+Version: 0.3.0
 Authors@R: c(
         person(given = 'YASUMOTO Atsushi', role = c('aut', 'cph', 'cre'), email = '[email protected]'),
         person(given = 'YOSHIDA Kenta', role = c('ctb')),
@@ -17,16 +17,17 @@ Description: A main function of this packages is
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 Depends: R(>= 3.1.2)
 Imports: curl,
     data.table,
     dplyr,
-    ggplot2,
+    DT,
     easycsv,
-    imager,
+    ggplot2,
+    htmltools,
+    knitr,
     matrixStats,
-    plotly,
     pipeR,
     PoiClaClu,
     png,
@@ -35,6 +36,7 @@ Imports: curl,
     scales,
     stringr,
     shiny,
+    shinyWidgets,
     tibble,
     tidyr,
     utils
@@ -56,15 +58,13 @@ Collate:
     'find_centers_kpp.R'
     'group_cluster.R'
     'mean.R'
+    'plot-shiny.R'
     'plot.R'
-    'plot_shiny.R'
-    'plotly.R'
+    'plot_gg.R'
     'print.R'
     'qntmap.R'
     'quantify.R'
     'read_cnd.R'
-    'read_map_beam.R'
-    'read_map_pos.R'
     'read_qnt.R'
     'read_qnt_elemw.R'
     'read_xmap.R'
@@ -78,6 +78,7 @@ Collate:
 Roxygen: list(markdown = TRUE)
 Suggests: 
     knitr,
+    pkgdown,
     rmarkdown,
     testthat
 VignetteBuilder: knitr

NAMESPACE

@@ -2,6 +2,8 @@
 
 S3method(mean,qntmap)
 S3method(pick,qm_xmap)
+S3method(plot,qm_cluster)
+S3method(plot,qm_raster)
 S3method(plot,qm_xmap)
 S3method(plot,qntmap)
 S3method(print,qntmap)
@@ -30,14 +32,18 @@ export(read_xmap)
 export(save4qm)
 export(segment)
 export(tidy_epma)
-import(shiny)
+importFrom(DT,dataTableOutput)
+importFrom(DT,datatable)
+importFrom(DT,formatRound)
+importFrom(DT,renderDT)
 importFrom(PoiClaClu,Classify)
 importFrom(data.table,fread)
 importFrom(data.table,fwrite)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,distinct)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,left_join)
@@ -49,55 +55,80 @@ importFrom(dplyr,right_join)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
+importFrom(dplyr,summarize_if)
 importFrom(dplyr,transmute)
 importFrom(dplyr,transmute_at)
 importFrom(dplyr,ungroup)
 importFrom(easycsv,choose_dir)
 importFrom(ggplot2,aes)
-importFrom(ggplot2,aes_string)
+importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,coord_fixed)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_rect)
-importFrom(ggplot2,geom_col)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_raster)
 importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggtitle)
-importFrom(ggplot2,scale_fill_gradientn)
+importFrom(ggplot2,guide_colorbar)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
+importFrom(ggplot2,scale_fill_gradient)
+importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_fill_viridis_c)
 importFrom(ggplot2,scale_y_reverse)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_classic)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,dev.copy)
 importFrom(grDevices,dev.off)
+importFrom(grDevices,nclass.FD)
 importFrom(grDevices,png)
 importFrom(grDevices,rgb)
-importFrom(graphics,hist)
 importFrom(graphics,pie)
 importFrom(graphics,plot)
-importFrom(imager,load.image)
+importFrom(grid,unit)
+importFrom(htmltools,br)
+importFrom(htmltools,tags)
+importFrom(knitr,kable)
 importFrom(matrixStats,rowMaxs)
 importFrom(matrixStats,weightedMedian)
 importFrom(pipeR,"%>>%")
 importFrom(pipeR,pipeline)
-importFrom(plotly,event_data)
-importFrom(plotly,ggplotly)
-importFrom(plotly,layout)
-importFrom(plotly,plot_ly)
-importFrom(plotly,plotlyOutput)
-importFrom(plotly,renderPlotly)
+importFrom(png,readPNG)
 importFrom(png,writePNG)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map2_dbl)
 importFrom(purrr,map_at)
 importFrom(purrr,map_dbl)
+importFrom(purrr,map_if)
 importFrom(purrr,map_int)
 importFrom(purrr,pmap)
 importFrom(purrr,walk2)
-importFrom(scales,gradient_n_pal)
+importFrom(rlang,sym)
 importFrom(scales,squish)
-importFrom(scales,viridis_pal)
+importFrom(shiny,brushOpts)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,fluidPage)
+importFrom(shiny,hoverOpts)
+importFrom(shiny,htmlOutput)
+importFrom(shiny,mainPanel)
+importFrom(shiny,numericInput)
+importFrom(shiny,observeEvent)
+importFrom(shiny,plotOutput)
+importFrom(shiny,reactive)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,renderPlot)
+importFrom(shiny,renderPrint)
+importFrom(shiny,renderUI)
+importFrom(shiny,req)
+importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
+importFrom(shiny,sidebarLayout)
+importFrom(shiny,sidebarPanel)
+importFrom(shiny,splitLayout)
+importFrom(shiny,uiOutput)
+importFrom(shinyWidgets,radioGroupButtons)
 importFrom(stats,coef)
 importFrom(stats,lm)
 importFrom(stats,lsfit)

NEWS.md

@@ -1,3 +1,22 @@
+# 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.
+    - Clustering result is supported.
+- `segment()`
+    - Only allows PNG format as an input. 
+      No more JPG nor BMP allowed.
+
 # qntmap 0.2.2
 
 ## Major changes