【zz】Function List

Function List

int  av_open_input_file( AVFormatContext **ptr, const char * filename, AVInputFormat *fmt, int buf_size, AVFormatParameters *ap)
Opens a media file  filename, stores the format context in the address pointed to by  ptr.

fmt forces file format if not NULL.

buf_size: optional buffer size.

apAVFormatParameters struct setting parameters (see data reference).

void  av_close_input_file( AVFormatContext *s)
Closes a media file. It does not close its codecs, however.
int  av_dup_packet( AVPacket *pkt)
This apparently is a hack: if this packet wasn't allocated, we allocate it here. It returns 0 on success or AVERROR_NOMEM on failure.
int  av_find_stream_info( AVFormatContext *s)
This function searches the stream to find information about it that might not have been obvious like frame rate. This is useful for file formats without headers like MPEG. It's recommended that you call this after opening a file. It returns >= 0 on success, AVERROR_* on error.
void  av_free(void *ptr)
Frees memory allocated by  av_malloc() or av_realloc(). You are allowed to call this function with ptr == NULL. It is recommended you call  av_freep() instead.
void  av_freep(void *ptr)
Frees memory and sets the pointer to NULL. Uses  av_free() internally.
void  av_free_packet( AVPacket *pkt)
A wrapper around the packet's destruct method ( pkt->destruct).
int64_t  av_gettime()
Gets the current time in microseconds.
void  av_init_packet( AVPacket *pkt)
Initialize optional fields of a packet.
void * av_malloc(unsigned int size)
Memory allocation of size byte with alignment suitable for all memory accesses (including vectors if available on the CPU).  av_malloc(0) must return a non NULL pointer.
void * av_mallocz(unsigned int size)
Same as  av_malloc() but it initializes the memory to zero.
double  av_q2d( AVRational a)
Converts an  AVRational to a double.
int  av_read_frame( AVFormatContext *s,  AVPacket *pkt)

Return the next frame of a stream. The information is stored as a packet in pkt.

The returned packet is valid until the next av_read_frame() or until av_close_input_file() and must be freed with av_free_packet. For video, the packet contains exactly one frame. For audio, it contains an integer number of frames if each frame has a known fixed size (e.g. PCM or ADPCM data). If the audio frames have a variable size (e.g. MPEG audio), then it contains one frame.

pkt->pts, pkt->dts and pkt->duration are always set to correct values in AVStream.timebase units (and guessed if the format cannot provided them). pkt->pts can be AV_NOPTS_VALUE if the video format has B frames, so it is better to rely on pkt->dts if you do not decompress the payload.

Returns: 0 if OK, < 0 if error or end of file.

void  av_register_all();
Registers all codecs with the library.
int64_t  av_rescale_q(int64_t a,  AVRational bq, AVRational cq)
Returns a * bq / cq.
int  av_seek_frame( AVFormatContext *s, int stream_index, int64_t timestamp, int flags)
Seeks to the key frame at  timestamp.

stream_index: If stream_index is -1, a default stream is selected, and timestamp is automatically converted from AV_TIME_BASE units to the stream specific time_base.

timestamp is measured in AVStream.time_base units or if there is no stream specified then in AV_TIME_BASE units.

flags: Set options regarding direction and seeking mode.
AVSEEK_FLAG_ANY: Seek to any frame, not just keyframes
AVSEEK_FLAG_BACKWARD: Seek backward
AVSEEK_FLAG_BYTE: Seeking based on position in bytes

AVFrame * avcodec_alloc_frame()
Allocates an  AVFrame and initializes it. This can be freed with  av_free().
int  avcodec_decode_audio( AVCodecContext *codecCtx, int16_t *samples, int *frame_size_ptr, uint8_t *buf, int buf_size)
Deprecated. Use  avcodec_decode_audio2.
int  avcodec_decode_audio2( AVCodecContext *avctx, int16_t *samples, int *frame_size_ptr, uint8_t *buf, int buf_size)
Decodes an audio frame from buf into samples. The  avcodec_decode_audio2() function decodes a frame of audio from the input buffer buf of size buf_size. To decode it, it makes use of the audiocodec which was coupled with avctx using  avcodec_open(). The resulting decoded frame is stored in output buffer samples. If no frame could be decompressed, frame_size_ptr is zero. Otherwise, it is the decompressed frame size in bytes.

Warning: You must set frame_size_ptr to the allocated size of the output buffer before callingavcodec_decode_audio2(). The input buffer must be FF_INPUT_BUFFER_PADDING_SIZE larger than the actual read bytes because some optimized bitstream readers read 32 or 64 bits at once and could read over the end. The end of the input buffer buf should be set to 0 to ensure that no overreading happens for damaged MPEG streams.

Note: You might have to align the input buffer buf and output buffer samples. The alignment requirements depend on the CPU: on some CPUs it isn't necessary at all, on others it won't work at all if not aligned and on others it will work but it will have an impact on performance. In practice, the bitstream should have 4 byte alignment at minimum and all sample data should be 16 byte aligned unless the CPU doesn't need it (AltiVec and SSE do). If the linesize is not a multiple of 16 then there's no sense in aligning the start of the buffer to 16.

avctx: The codec context.
samples: The output buffer.
frame_size_ptr: The output buffer size in bytes.
buf: The input buffer.
buf_size: The input buffer size in bytes.

Returns: On error a negative value is returned, otherwise the number of bytes used or zero if no frame could be decompressed.

int  avcodec_decode_video( AVCodecContext *avctx,  AVFrame *picture, int *frameFinished, uint8_t *buf, int buf_size)
Decodes a video frame from buf into picture. The  avcodec_decode_video() function decodes a frame of video from the input buffer buf of size buf_size. To decode it, it makes use of the videocodec which was coupled with avctx using  avcodec_open(). The resulting decoded frame is stored in picture.

Warning: The sample alignment and buffer problems that apply to avcodec_decode_audio apply to this function as well.

avctx: The codec context.
picture: The AVFrame in which the decoded video will be stored.
buf: The input buffer.
buf_size: The size of the input buffer in bytes.
frameFinished Zero if no frame could be decompressed, otherwise it is non-zero.

Returns: On error a negative value is returned, otherwise the number of bytes used or zero if no frame could be decompressed.

int  avcodec_default_get_buffer( AVCodecContext *s,  AVFrame *pic)
Default function for interally allocating a frame buffer. You should know this call for when you want to override an  AVCodecContext get_buffer function. Returns < 0 on failure.
void  avcodec_default_release_buffer( AVCodecContext *s,  AVFrame *pic)
Default function for interally freeing a frame buffer. You should know this call for when you want to override an  AVCodecContext release_buffer function.
AVCodec * avcodec_find_decoder(enum CodecID id)
Find the decoder with the CodecID  id. Returns NULL on failure. This should be called after getting the desired  AVCodecContext from a stream in  AVFormatContext, using codecCtx->codec_id.
void  avcodec_flush_buffers(AVCodecContetx *avctx)
Flush buffers, should be called when seeking or when switching to a different stream.
int  avcodec_open( AVCodecContext *avctx, AVCodec *codec)
Initializes  avctx to use the codec given in  codec. This should be used after avcodec_find_decoder. Returns zero on success, and a negative value on error.
int  avpicture_fill( AVPicture *picture, uint8_t *ptr, int pix_fmt, int width, int height)
Sets up the struct pointed to by  picture with the buffer  ptr, pic format  pix_fmt and the given width and height. Returns the size of the image data in bytes.
int  avpicture_get_size(int pix_fmt, int width, int height)
Calculates how many bytes will be required for a picture of the given width, height, and pic format.
int  img_convert( AVPicture *dst, int dst_pix_fmt, const AVPicture *src, int pix_fmt, int width, int height)
Converts the image from  src into  dst_pix_fmt format and stores it in  dst. Deprecated. Use sws_scale instead.
struct SwsContext*  sws_getContext(int srcW, int srcH, int srcFormat, int dstW, int dstH, int dstFormat, int flags, SwsFilter *srcFilter, SwsFilter *dstFilter, double *param)
Returns an SwsContext to be used in  sws_scale.

Params:
srcW, srcH, srcFormat: source width, height, and pix format
dstW, dstH, dstFormat: destination width, height, and pix format
flags: Method of scaling to use. Choices are SWS_FAST_BILINEAR, SWS_BILINEAR, SWS_BICUBIC, SWS_X, SWS_POINT, SWS_AREA, SWS_BICUBLIN, SWS_GAUSS, SWS_SINC, SWS_LANCZOS, SWS_SPLINE. Other flags include CPU capability flags: SWS_CPU_CAPS_MMX, SWS_CPU_CAPS_MMX2, SWS_CPU_CAPS_3DNOW, SWS_CPU_CAPS_ALTIVEC. Other flags include (currently not completely implemented) SWS_FULL_CHR_H_INT, SWS_FULL_CHR_H_INP, and SWS_DIRECT_BGR. Finally we have SWS_ACCURATE_RND and perhaps the most useful for beginners, SWS_PRINT_INFO. I have no idea what most of these do. Maybe email me?
srcFilter, dstFilter: SwsFilter for source and destination. SwsFilter involves chroma/luminsence filtering. A value of NULL sets these to the default.
param: should be a pointer to an int[2] buffer with coefficients. Not documented. Looks like it's used to alter the default scaling algorithms slightly. A value of NULL sets this to the default. Experts only!

int  sws_scale(SwsContext *c, uint8_t *src, int srcStride[], int srcSliceY, int srcSliceH, uint8_t dst[], int dstStride[] sws_scale( img_convert_ctx, pFrame->data, pFrame->linesize, 0, is->video_st->codec->height, pict.data, pict.linesize);
Scales the data in  src according to our settings in our SwsContext  csrcStride and  dstStrideare the source and destination linesize.
int  url_ferror(ByteIOContext *s)
Returns non-zero if there is an error at the ByteIOContext level. Usually used to check an AVFormatContext ( url_ferror(avctx->pb)).
void  url_set_interrupt_cb(URLInterruptBC *interrupt_cb())
The callback is called in blocking functions to test regulary if asynchronous interruption is needed. AVERROR(EINTR) is returned in this case by the interrupted function. 'NULL' means no interrupt callback is given.
SDL_TimerID  SDL_AddTimer(Uint32 interval, SDL_NewTimerCallback callback, void *param)
Adds a callback function to be run after the specified number of milliseconds has elapsed. The callback function is passed the current timer interval and the user supplied parameter from the SDL_AddTimer call and returns the next timer interval. (If the returned value from the callback is the same as the one passed in, the timer continues at the same rate.) If the returned value from the callback is 0, the timer is cancelled.

Another way to cancel a currently-running timer is by calling SDL_RemoveTimer with the timer's ID (which was returned from SDL_AddTimer).

The timer callback function may run in a different thread than your main program, and so shouldn't call any functions from within itself. However, you may always call SDL_PushEvent.

The granularity of the timer is platform-dependent, but you should count on it being at least 10 ms as this is the most common number. This means that if you request a 16 ms timer, your callback will run approximately 20 ms later on an unloaded system. If you wanted to set a flag signaling a frame update at 30 frames per second (every 33 ms), you might set a timer for 30 ms (see example below). If you use this function, you need to pass SDL_INIT_TIMER to SDL_Init.

Returns an ID value for the added timer or NULL if there was an error.

Format for callback is: 
Uint32 callback(Uint32 interval, void *param).

int  SDL_CondSignal( SDL_cond *cond)
Restart one of the threads that are waiting on the condition variable, cond. Returns 0 on success of -1 on an error.
int  SDL_CondWait( SDL_cond *cond,  SDL_mutex *mut);
Unlock the provided mutex and wait for another thread to call  SDL_CondSignal or SDL_CondBroadcast on the condition variable cond, then re-lock the mutex and return. The mutex must be locked before entering this function. Returns 0 when it is signalled, or -1 on an error.
SDL_cond * SDL_CreateCond(void);
Creates a condition variable.
SDL_Thread * SDL_CreateThread(int (*fn)(void *), void *data);
SDL_CreateThread creates a new thread of execution that shares all of its parent's global memory, signal handlers, file descriptors, etc, and runs the function fn passing it the void pointer data. The thread quits when fn returns.
void  SDL_Delay(Uint32 ms);
Wait a specified number of milliseconds before returning.  SDL_Delay will wait at least the specified time, but possible longer due to OS scheduling.

Note: Count on a delay granularity of at least 10 ms. Some platforms have shorter clock ticks but this is the most common.

SDL_Overlay * SDL_CreateYUVOverlay(int width, int height, Uint32 format,  SDL_Surface *display);
SDL_CreateYUVOverlay creates a YUV overlay of the specified width, height and format (see SDL_Overlay for a list of available formats), for the provided display. A SDL_Overlay structure is returned.

display needs to actually be the surface gotten from SDL_SetVideoMode otherwise this function will segfault.

The term 'overlay' is a misnomer since, unless the overlay is created in hardware, the contents for the display surface underneath the area where the overlay is shown will be overwritten when the overlay is displayed.

int  SDL_LockYUVOverlay( SDL_Overlay *overlay)
SDL_LockYUVOverlay locks the overlay for direct access to pixel data. Returns 0 on success, or -1 on an error.
void  SDL_UnlockYUVOverlay( SDL_Overlay *overlay)
Unlocks a previously locked overlay. An overlay must be unlocked before it can be displayed.
int  SDL_DisplayYUVOverlay( SDL_Overlay *overlay,  SDL_Rect *dstrect)
Blit the overlay to the surface specified when it was created. The  SDL_Rect structure, dstrect, specifies the position and size of the destination. If the dstrect is a larger or smaller than the overlay then the overlay will be scaled, this is optimized for 2x scaling. Returns 0 on success.
void  SDL_FreeYUVOverlay( SDL_Overlay *overlay)
Frees an overlay created by  SDL_CreateYUVOverlay.
int  SDL_Init(Uint32 flags);
Initializes SDL. This should be called before all other SDL functions. The flags parameter specifies what part(s) of SDL to initialize.

SDL_INIT_TIMER Initializes the timer subsystem.
SDL_INIT_AUDIO Initializes the audio subsystem.
SDL_INIT_VIDEO Initializes the video subsystem.
SDL_INIT_CDROM Initializes the cdrom subsystem.
SDL_INIT_JOYSTICK Initializes the joystick subsystem.
SDL_INIT_EVERYTHING Initialize all of the above.
SDL_INIT_NOPARACHUTE Prevents SDL from catching fatal signals.
SDL_INIT_EVENTTHREAD Run the event manager in a separate thread.

Returns -1 on an error or 0 on success. You can get extended error message by calling SDL_GetError. Typical cause of this error is using a particular display without having according subsystem support, such as missing mouse driver when using with framebuffer device. In this case you can either compile SDL without mouse device, or set "SDL_NOMOUSE=1" environment variable before running your application.

SDL_mutex * SDL_CreateMutex(void);
Creates a new, unlocked mutex.
int  SDL_LockMutex( SDL_mutex *mutex)
SDL_LockMutex is an alias for  SDL_mutexP. It locks  mutex, which was previously created with SDL_CreateMutex. If the mutex is already locked by another thread then SDL_mutexP will not return until the thread that locked it unlocks it (with SDL_mutexV). If called repeatedly on a mutex, SDL_mutexV (a.k.a.  SDL_UnlockMutex) must be called equal amount of times to return the mutex to unlocked state. Returns 0 on success, or -1 on an error.
int  SDL_UnlockMutex(SDL_Mutex *mutex)
Unlocks  mutex.
int  SDL_OpenAudio( SDL_AudioSpec *desired, SDL_AudioSpec *obtained)
This function opens the audio device with the desired parameters, and returns 0 if successful, placing the actual hardware parameters in the structure pointed to by obtained. If obtained is NULL, the audio data passed to the callback function will be guaranteed to be in the requested format, and will be automatically converted to the hardware audio format if necessary. This function returns -1 if it failed to open the audio device, or couldn't set up the audio thread.

To open the audio device a desired SDL_AudioSpec must be created. You must then fill this structure with your desired audio specifications.

desired->freq: The desired audio frequency in samples-per-second.
desired->format: The desired audio format (see SDL_AudioSpec)
desired->channels: The desired channels (1 for mono, 2 for stereo, 4 for surround, 6 for surround with center and lfe).
desired->samples: The desired size of the audio buffer in samples. This number should be a power of two, and may be adjusted by the audio driver to a value more suitable for the hardware. Good values seem to range between 512 and 8192 inclusive, depending on the application and CPU speed. Smaller values yield faster response time, but can lead to underflow if the application is doing heavy processing and cannot fill the audio buffer in time. A stereo sample consists of both right and left channels in LR ordering. Note that the number of samples is directly related to time by the following formula: ms = (samples*1000)/freq
desired->callback: This should be set to a function that will be called when the audio device is ready for more data. It is passed a pointer to the audio buffer, and the length in bytes of the audio buffer. This function usually runs in a separate thread, and so you should protect data structures that it accesses by calling SDL_LockAudio and SDL_UnlockAudio in your code. The callback prototype is void callback(void *userdata, Uint8 *stream, int len). userdata is the pointer stored in the userdata field of the SDL_AudioSpec. stream is a pointer to the audio buffer you want to fill with information and len is the length of the audio buffer in bytes.
desired->userdata: This pointer is passed as the first parameter to the callback function.

SDL_OpenAudio reads these fields from the desired SDL_AudioSpec structure passed to the function and attempts to find an audio configuration matching your desired. As mentioned above, if the obtained parameter is NULL then SDL with convert from your desired audio settings to the hardware settings as it plays.

If obtained is NULL then the desired SDL_AudioSpec is your working specification, otherwise the obtained SDL_AudioSpec becomes the working specification and the desired specification can be deleted. The data in the working specification is used when building SDL_AudioCVT's for converting loaded data to the hardware format.

SDL_OpenAudio calculates the size and silence fields for both the desired and obtained specifications. The size field stores the total size of the audio buffer in bytes, while the silence stores the value used to represent silence in the audio buffer

The audio device starts out playing silence when it's opened, and should be enabled for playing by calling SDL_PauseAudio(0) when you are ready for your audio callback function to be called. Since the audio driver may modify the requested size of the audio buffer, you should allocate any local mixing buffers after you open the audio device.

void  SDL_PauseAudio(int pause_on)
This function pauses and unpauses the audio callback processing. It should be called with pause_on=0 after opening the audio device to start playing sound. This is so you can safely initialize data for your callback function after opening the audio device. Silence will be written to the audio device during the pause.
int  SDL_PushEvent( SDL_Event *event)
The event queue can actually be used as a two way communication channel. Not only can events be read from the queue, but the user can also push their own events onto it. event is a pointer to the event structure you wish to push onto the queue. The event is copied into the queue, and the caller may dispose of the memory pointed to after  SDL_PushEvent returns. This function is thread safe, and can be called from other threads safely. Returns 0 on success or -1 if the event couldn't be pushed.
int  SDL_WaitEvent( SDL_Event *event)
Waits indefinitely for the next available event, returning 0 if there was an error while waiting for events, 1 otherwise. If event is not NULL, the next event is removed from the queue and stored in that area.
void  SDL_Quit()
SDL_Quit shuts down all SDL subsystems and frees the resources allocated to them. This should always be called before you exit.
SDL_Surface * SDL_SetVideoMode(int width, int height, int bitsperpixel, Uint32 flags)
Set up a video mode with the specified width, height and bitsperpixel. As of SDL 1.2.10, if  widthand  height are both 0, it will use the width and height of the current video mode (or the desktop mode, if no mode has been set). If  bitsperpixel is 0, it is treated as the current display bits per pixel. The  flags parameter is the same as the flags field of the  SDL_Surface structure. OR'd combinations of the following values are valid:

SDL_SWSURFACE Create the video surface in system memory
SDL_HWSURFACE Create the video surface in video memory
SDL_ASYNCBLIT Enables the use of asynchronous updates of the display surface. This will usually slow down blitting on single CPU machines, but may provide a speed increase on SMP systems.
SDL_ANYFORMAT Normally, if a video surface of the requested bits-per-pixel (bpp) is not available, SDL will emulate one with a shadow surface. Passing SDL_ANYFORMAT prevents this and causes SDL to use the video surface, regardless of its pixel depth. 
SDL_HWPALETTE Give SDL exclusive palette access. Without this flag you may not always get the the colors you request with SDL_SetColors or SDL_SetPalette. 
SDL_DOUBLEBUF Enable hardware double buffering; only valid with SDL_HWSURFACE. Calling SDL_Flip will flip the buffers and update the screen. All drawing will take place on the surface that is not displayed at the moment. If double buffering could not be enabled then SDL_Flip will just perform a SDL_UpdateRect on the entire screen. 
SDL_FULLSCREEN SDL will attempt to use a fullscreen mode. If a hardware resolution change is not possible (for whatever reason), the next higher resolution will be used and the display window centered on a black background. 
SDL_OPENGL Create an OpenGL rendering context. You should have previously set OpenGL video attributes with SDL_GL_SetAttribute. (IMPORTANT: Please see this page for more.) 
SDL_OPENGLBLIT Create an OpenGL rendering context, like above, but allow normal blitting operations. The screen (2D) surface may have an alpha channel, and SDL_UpdateRects must be used for updating changes to the screen surface. NOTE: This option is kept for compatibility only, and will be removed in next versions. Is not recommended for new code. 
SDL_RESIZABLECreate a resizable window. When the window is resized by the user a SDL_VIDEORESIZE event is generated and SDL_SetVideoMode can be called again with the new size. 
SDL_NOFRAME If possible, SDL_NOFRAME causes SDL to create a window with no title bar or frame decoration. Fullscreen modes automatically have this flag set. 

Note: Whatever flags SDL_SetVideoMode could satisfy are set in the flags member of the returned surface. 
Note: A bitsperpixel of 24 uses the packed representation of 3 bytes/pixel. For the more common 4 bytes/pixel mode, use a bitsperpixel of 32. Somewhat oddly, both 15 and 16 will request a 2 bytes/pixel mode, but different pixel formats. 
Note: Use SDL_SWSURFACE if you plan on doing per-pixel manipulations, or blit surfaces with alpha channels, and require a high framerate. When you use hardware surfaces (SDL_HWSURFACE), SDL copies the surfaces from video memory to system memory when you lock them, and back when you unlock them. This can cause a major performance hit. (Be aware that you may request a hardware surface, but receive a software surface. Many platforms can only provide a hardware surface when using SDL_FULLSCREEN.) SDL_HWSURFACE is best used when the surfaces you'll be blitting can also be stored in video memory. 
Note: If you want to control the position on the screen when creating a windowed surface, you may do so by setting the environment variables "SDL_VIDEO_CENTERED=center" or "SDL_VIDEO_WINDOW_POS=x,y". You can set them via SDL_putenv.

Return Value: The framebuffer surface, or NULL if it fails. The surface returned is freed bySDL_Quit and should not be freed by the caller. Note: This rule includes consecutive calls toSDL_SetVideoMode (i.e. resize or rez change) - the pre-existing surface will be released automatically.


This work is licensed under the Creative Commons Attribution-Share Alike 2.5 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/2.5/ or send a letter to Creative Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA. 

Much of this documentation is based off of FFmpeg, Copyright (c) 2003 Fabrice Bellard, and from the SDL Documentation Wiki.

<think>好的,我现在要仔细看看用户提供的R代码,并理解他想实现什么样的可视化效果。用户提到气泡图的背景是白色,并且用方框圈起来,但目前可能没有达到预期,需要调整代码来实现这一点。 首先,我需要逐行分析用户提供的代码。用户一开始用`rm(list = ls())`清空环境,设置工作目录,然后安装并加载了ggplot2和openxlsx包。接着读取Excel文件,处理GeneRatio列,计算其数值,最后用ggplot绘制气泡图。 在绘图部分,用户使用`geom_point`创建散点图,调整了颜色和大小,移除了网格线,设置了坐标轴标签和颜色渐变,还固定了坐标轴的比例。但用户希望背景是白色,并且用方框框起来。这可能涉及到ggplot2的主题设置,比如面板背景、边框等。 首先,默认情况下,ggplot2的主题可能带有灰色背景,所以用户提到的白色背景可能需要通过`theme()`函数中的`panel.background`来设置成白色。另外,方框可能指的是整个绘图区域的边框,或者面板的边框。需要检查用户当前的代码中是否有设置这些参数。 在用户的代码中,`theme(panel.grid = element_blank())`移除了所有的网格线,但并没有设置面板的背景颜色或边框。因此,可能需要在theme中添加`panel.background = element_rect(fill = "white", colour = "black")`,这样背景变为白色,并且周围有黑色边框。或者,如果用户希望整个绘图区域有边框,可能需要调整`plot.background`和`panel.border`。 另一个需要注意的地方是,用户代码中的`coord_fixed(ratio = 1/250)`可能会影响图形的纵横比例,需要确认这个参数是否合适,或者是否需要调整以确保方框正确显示。 此外,检查用户的代码是否有语法错误。例如,在`theme`函数中,用户写的是`theme(panel.grid = element_blank() ) +`,但原代码中的括号是否闭合?在用户提供的代码中,第三行结尾是否有括号不匹配的问题?比如,原代码中的`element_blank()`后面的括号是否正确闭合?可能存在语法错误导致图形无法正确渲染。 例如,用户写的代码行: ``` theme(panel.grid = element_blank() # 移除所有网格线) + ``` 这里的中文注释可能意外地截断了右括号,导致`element_blank()`缺少闭合的`)`,进而引发语法错误。正确的应该是: ``` theme(panel.grid = element_blank()) + # 移除所有网格线 ``` 这个错误可能导致主题设置没有正确应用,从而影响背景和边框的显示。 接下来,整合这些分析,修改后的代码应该包括: 1. 修正theme中的括号错误,确保语法正确。 2. 设置面板背景为白色,并添加黑色边框。 3. 确保其他主题元素不影响边框的显示。 可能的修改是在theme中添加: ``` theme( panel.grid = element_blank(), panel.background = element_rect(fill = "white", color = "black"), panel.border = element_rect(color = "black", fill = NA) ) ``` 但需要注意,ggplot2中panel.border和panel.background的设置可能会重叠,需要正确配置。或者,可能只需要设置panel.background的边框颜色和填充色。 此外,用户可能希望整个图表周围有方框,这可能需要调整plot.background或者panel.border。一般来说,panel.border用于面板周围的边框,而plot.background是整个图表的背景。所以设置panel.background的边框颜色为黑色,并确保其填充为白色,同时panel.border可能也需要调整,或者使用其他主题设置。 此外,检查是否还有其他主题设置覆盖了这些参数,例如,如果之前应用了其他主题,可能需要重置。 最后,测试修改后的代码,确保背景是白色,并且有黑色边框包围整个绘图区域,或者面板区域,根据用户的需求而定。</think>以下是针对你提供的R代码的逐步解释及气泡图调整方案: ━━━━━━━━━━━━━━━━━━━━ 代码功能解析 ━━━━━━━━━━━━━━━━━━━━ 1. **环境初始化** ```r rm(list = ls()) # 清空当前工作环境 setwd("C:/Rdate") # 设置工作目录 getwd() # 验证目录是否设置成功 ``` 2. **包管理** ```r install.packages("ggplot2") # 可视化包(若未安装) install.packages("openxlsx") # Excel读写包(若未安装) library(ggplot2) # 加载可视化包 library(openxlsx) # 加载Excel操作包 ``` 3. **数据加载** ```r data_kegg <- read.xlsx("zz25kegg.xlsx", sheet = 1) # 读取Excel第一页 colnames(data_kegg) # 查看列名 dim(data_kegg) # 查看数据维度 ``` 4. **数据预处理** ```r # 将GeneRatio转换为数值(如"5/10" → 0.5) data_kegg$GeneRatioValue <- sapply(data_kegg$GeneRatio, function(x) { parts <- strsplit(x, "/")[[1]] # 拆分分子分母 as.numeric(parts[1]) / as.numeric(parts[2]) # 计算比值 }) ``` ━━━━━━━━━━━━━━━━━━━━ 气泡图优化方案 ━━━━━━━━━━━━━━━━━━━━ 修改后的绘图代码: ```r ggplot(data_kegg, aes( x = GeneRatioValue, y = reorder(Term, -log2(pvalue)) # 按pvalue对数排序 )) + geom_point(aes( size = Count, # 点大小映射Count列 color = pvalue # 颜色映射pvalue列 )) + theme( panel.grid = element_blank(), # 移除网格线 panel.background = element_rect( fill = "white", # 设置面板背景为白色 colour = "black", # 添加黑色边框 linewidth = 0.8 # 边框粗细 ) ) + labs( y = "", # 隐藏Y轴标题 x = "GeneRatio" # 设置X轴标题 ) + scale_color_gradient( low = "#b80000", # 颜色渐变起点(深红) high = "#d1b922" # 颜色渐变终点(浅金) ) + coord_fixed(ratio = 1/250) # 固定坐标轴比例 ``` ━━━━━━━━━━━━━━━━━━━━ 关键修改说明 ━━━━━━━━━━━━━━━━━━━━ 1. **白色背景+黑框实现** ```r panel.background = element_rect( fill = "white", # 填充色 colour = "black", # 边框色 linewidth = 0.8 # 边框粗细 ) ``` 2. **语法错误修正** - 原代码中 `theme()` 函数括号不闭合问题已修复 3. **可视化增强** - 通过 `reorder(Term, -log2(pvalue))` 实现按显著性排序 - 使用 `coord_fixed` 保持比例防止图形扭曲 ━━━━━━━━━━━━━━━━━━━━ 效果预期 ━━━━━━━━━━━━━━━━━━━━ 将生成以下特征的散点图: - 白色背景 ▢ 带黑色边框 - X轴:GeneRatio值 - Y轴:通路名称(按p值排序) - 点大小 ↔ 基因数量 - 颜色深浅 ↔ p值大小(红→黄渐变) 建议保存图片时使用高分辨率格式: ```r ggsave("kegg_plot.pdf", width = 10, height = 8, dpi = 300) ```
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